Theoretical and Applied Genetics

, Volume 132, Issue 1, pp 1–25 | Cite as

Development and use of chromosome segment substitution lines as a genetic resource for crop improvement

  • Divya Balakrishnan
  • Malathi Surapaneni
  • Sukumar Mesapogu
  • Sarla NeelamrajuEmail author
Review Article


Key message

CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits.


Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.



Chromosome arm substitution lines


Candidate introgression lines


Chromosome segment introgression lines


Next-generation NIL (near isogenic line) library


Recombinant chromosome substitution lines


Small-segment chromosome translocations and introgression


Single-segment substitution lines


Stepped aligned inbred recombinant strains



Authors acknowledge ICAR National Professor Project (F. No. Edn/27/4/NP/2012-HRD) Indian Council for Agricultural Research, Government of India, for financial support. Authors are grateful to Dr. D.S. Brar for critically reviewing an earlier version of the manuscript and constant encouragement. We thank Director, ICAR-IIRR, for support.

Compliance with ethical standards

Conflict of interest

Authors declare that there is no conflict of interest.

Ethical standard

The authors declare that the experiments comply with the current laws of the country in which they were performed and are in compliance with ethical standards.

Supplementary material

122_2018_3219_MOESM1_ESM.xlsx (29 kb)
Supplementary material 1 (XLSX 28 kb)
122_2018_3219_MOESM2_ESM.docx (17 kb)
Supplementary material 2 (DOCX 17 kb)


  1. Adachi S, Tsusru Y, Kondo M, Yamamoto T, Arai SY, Ando T, Ookawa T, Yano M, Hirasawa T (2010) Characterization of a rice variety with high hydraulic conductance and identification of the chromosome region responsible using chromosome segment substitution lines. Ann Bot 106:803–811PubMedPubMedCentralGoogle Scholar
  2. Ali ML, Sanchez PL, Si-bin Yu, Lorieu M, Eizenga GC (2010) Chromosome segment substitution lines: a powerful tool for the introgression of valuable genes from Oryza wild species into cultivated rice (O. sativa). Rice 3:218–234Google Scholar
  3. Allard RW (1960) Principles of plant breeding. Wiley, LondonGoogle Scholar
  4. Alpert KB, Tanskley SD (1996) High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw22: a major fruit weight quantitative trait locus in tomato. Proc Natl Acad Sci USA 93(26):15503–15507PubMedGoogle Scholar
  5. Ando T, Yamamoto T, Shimizu T, Ma X, Shomura A, Takeuchi Y, Lin S, Yano M (2008) Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. Theor Appl Genet 116:881–890PubMedGoogle Scholar
  6. Anis G, Zhang Y, Xu X, Fiaz S, Wu W, Rahman MH, Riaz A, Chen D, Shen X, Zhan X, Cao L, Cheng S (2018) QTL analysis for rice seedlings under nitrogen deficiency using chromosomal segment substitution lines. Pak J Bot 50(2):537–544Google Scholar
  7. Arbelaez JD, Moreno LT, Singh N, Tung C, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M, McCouch S (2015) Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon in a common recurrent parent, O. sativa cv Curinga. Mol Breed 35:81. CrossRefPubMedPubMedCentralGoogle Scholar
  8. Ayling S, Lorieux M (2010) The shortest path to CSSL selection agrigenomics world congress, July 8–9 2010. Belgium, BrusselsGoogle Scholar
  9. Bai W, Zhang H, Zhang Z, Teng F, Wang L, Tao Y, Zheng Y (2010) The evidence for non-additive effect as the main genetic component of plant height and ear height in maize using introgression line populations. Plant Breed 129:376–384Google Scholar
  10. Baxter CJ, Carrari F, Bauke A, Overy S, Hill SA, Quick PW, Fernie AR, Sweetlove LJ (2005) Fruit carbohydrate metabolism in an introgression line of tomato with increased fruit soluble solids. Plant Cell Physiol 46:425–437PubMedGoogle Scholar
  11. Benavente E, Cifuentes M, Dusautoir JC, David J (2008) The use of cytogenetic tools for studies in the crop-to-wild gene transfer scenario. Cytogenet Genome Res 120:384–395PubMedGoogle Scholar
  12. Bermudez L, Urias U, Milstein D, Kamenetzky L, Asis R, Fernie AR, Van Sluys MA, Carrari F, Rossi M (2008) A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit. J Exp Bot 59(10):2875–2890PubMedPubMedCentralGoogle Scholar
  13. Bernacchi D, Beck-Bunn T, Emmatty D, Eshed Y et al (1998) Advanced backcross QTL analysis of tomato II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium. Theor Appl Genet 97:170–180Google Scholar
  14. Bian J, Jiang L, Liu LL, Wei XJ, Xiao YH, Zhang LJ, Zhao ZG, Zhai HQ, Wan JM (2010) Construction of a new set of rice chromosome segment substitution lines and identification of grain weight and related traits QTLs. Breed Sci 60:305–313Google Scholar
  15. Bian J, He H, Shi H, Zhu G, Li C, Zhu C et al (2014) Quantitative trait loci mapping for flag leaf traits in rice using a chromosome segment substitution line population. Plant Breed 133:203–209Google Scholar
  16. Brown AHD, Munday J, Oram RN (1988) Use of isozyme-marked segments from wild barley (Hordeum spontaneum) in barley breeding. Plant Breed 100:280–288Google Scholar
  17. Brozynska M, Furtado A, Henry RJ (2016) Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotech J 14:1070–1085Google Scholar
  18. Burnham CR (1966) Cytogenetics in plant improvement. In: Kenneth JF (ed) Plant breeding. The Iowa State University Press, Ames, pp 139–188Google Scholar
  19. Burns MJ, Barnes SR, Bowman JG, Clarke MHE, Werner CP, Kearsey MJ (2003) QTL analysis of an intervarietal set of substitution lines in Brassica napus: (i) seed oil content and fatty acid composition. Heredity 90:39–48PubMedGoogle Scholar
  20. Canady MA, Vladimir M, Roger TC (2005) A library of Solanum lycopersicoides introgression lines in cultivated tomato. Genome 48:685–697PubMedGoogle Scholar
  21. Cao Z, Wang P, Zhu X, Chen H, Zhang T (2014) SSR marker assisted improvement of fiber qualities in Gossypium hirsutum using G. barbadense introgression lines. Theor Appl Genet 127:587–594PubMedGoogle Scholar
  22. Castaneda-Álvarez NP, Khoury CK, Achicanoy HA, Bernau V, Dempewolf H, Eastwood RJ, Guarino L, Harker RH, Jarvis A, Maxted N, Müller JV, Ramirez-Villegas J, Sosa CC, Struik PC, Vincent H, Toll J (2016) Global conservation priorities for crop wild relatives. Nat Plants. CrossRefPubMedGoogle Scholar
  23. Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11:215–221PubMedGoogle Scholar
  24. Cheema KK, Bains NS, Mangat GS, Das A, Vikal Y, Brar DS et al (2008) Development of high yielding IR64 × Oryza rufipogon (Griff) introgression lines and identification of introgressed alien chromosome segments using markers. Euphytica 160:401–409Google Scholar
  25. Chen J, Hafeez URB, Chen D, Liu G, Zheng K, Zhuang J (2006) Development of chromosomal segment substitution lines from a backcross recombinant inbred population of interspecific rice cross. Rice Sci 13:15–21Google Scholar
  26. Chen QQ, Mu JX, Zhou HJ, Yu SB (2007) Genetic effect of japonica alleles detected in indica candidate introgression lines. Sci Agri Sin 40:2379–2387Google Scholar
  27. Chen J, Huang D-R, Wang L, Guang-Jie Liu G-J, Zhuang J-Y (2010) Identification of quantitative trait loci for resistance to whitebacked planthopper, Sogatella furcifera, from an interspecific cross Oryza sativa × O. rufipogon. Breed Sci 60:153–159Google Scholar
  28. Chen H, Xie W, He H, Yu H, Chen W, Li J, Yu R, Yao Y, Zhang W, He Y, Tang X, Zhou F, Deng XW, Zhang Q (2013) A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant 7:541–553PubMedGoogle Scholar
  29. Chen J, Li X, Cheng C, Wang Y, Qin M, Zhu H et al (2014) Characterization of epistatic interaction of QTLs LH8 and EH3 controlling heading date in rice. Sci Rep 4:4263PubMedPubMedCentralGoogle Scholar
  30. Cheng J, He Y, Zhan C, Yang B, Xu E, Zhang H, Wang Z (2016) Identification and characterization of quantitative trait loci for shattering in japonica rice landrace Jiucaiqing from Taihu Lake Valley. Plant Genome, China. CrossRefGoogle Scholar
  31. Chetelat RT, Meglic V (2000) Molecular mapping of chromosome segments introgressed from Solanum lycopersicoides into cultivated tomato (Lycopersicon esculentum). Theor Appl Genet 100:232–241Google Scholar
  32. Chitwood DH, Kumar R, Headland LR, Ranjan A, Covington MF, Ichihashi Y et al (2013) A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. Plant Cell 25:2465–2481PubMedPubMedCentralGoogle Scholar
  33. Chutimanukul P, Kositsup B, Plaimas K, Buaboocha T, Siangliw M, Toojinda T, Comai L, Chadchawan S (2018) Photosynthetic responses and identification of salt tolerance genes in a chromosome segment substitution line of ‘Khao Dawk Mali 105’ rice. Environ Exp Bot. CrossRefGoogle Scholar
  34. De Leon TB, Linscombe S, Subudhi PK (2017) Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace ‘Pokkali’. PLoS ONE 12(4):e0175361PubMedPubMedCentralGoogle Scholar
  35. Di Matteo A, Sacco A, Anacleria M, Pezzotti M, Delledonne M, Ferrarini A et al (2010) The ascorbic acid content of tomato fruits is associated with the expression of genes involved in pectin degradation. BMC Plant Biol 10:163PubMedPubMedCentralGoogle Scholar
  36. Dijkstra EW (1959) A note on two problems in connexion with graphs. Numer Math 1:269–271Google Scholar
  37. Doi K, Iwata N, Yosimura A (1997) The construction of chromosome substitution lines of African rice (Oryza glaberrima Steud) in the background of japonica rice (O. sativa L.). Rice Genet Newsl 14:39–41Google Scholar
  38. Ebitani T, Takeuchi Y, Nonoue Y, Yamamoto T, Takeuchi K, Yano M (2005) Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice Cultivar ‘Kasalath’ in a genetic background of japonica elite cultivar ‘Koshihikari. Breed Sci 55:65–73Google Scholar
  39. Ecke W, Kampouridis A, Kubon KZ, Hirsch AC (2015) Identification and genetic characterization by high-throughput SNP analysis of intervarietal substitution lines of rapeseed (Brassica napus L.) with enhanced embryogenic potential. Theor Appl Genet 128:587–603PubMedPubMedCentralGoogle Scholar
  40. Eduardo I, Arus P, Monforte AJ (2005) Development of a genomic library of near isogenic lines (NILs) in melon (Cucumis melo L.) from the exotic accession PI 161375. Theor Appl Genet 112:139–148PubMedGoogle Scholar
  41. Eduardo I, Arus P, Monforte AJ, Obando J, Fernandez JP, Martinez JA, Alarcon AL, Alvarez JM, Vander KE (2007) Estimating the genetic architecture of fruit quality traits in melon (Cucumis melo L.) using a genomic library of near-isogenic lines. J Am Soc Hortic Sci 132:80–89Google Scholar
  42. Eshed Y, Zamir D (1994) A genomic library of Lycopersicon pennellii in L esculentum: a tool for fine mapping of genes. Euphytica 79:175–179Google Scholar
  43. Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141:1147–1162PubMedPubMedCentralGoogle Scholar
  44. Eshed Y, Bu-Abied M, Saranga Y, Zamir D (1992) Lycopersicon esculentum lines containing small overlapping introgressions from Lycopersicon pennellii. Theor Appl Genet 83:1027–1034PubMedGoogle Scholar
  45. Falke KC, Suni TZ, Hackauf B, Korzun V, Schondelmaier J, Wilde P, Wehling P, Wortmann H, Mank J, van der Rouppe VJ, Maure H, Miedane T, Geiger HH (2008) Establishment of introgression libraries in hybrid rye (Secale cereale L.) from an Iranian primitive accession as a new tool for rye breeding and genomics. Theor Appl Genet 117:641–652PubMedGoogle Scholar
  46. Falke KC, Miedaner T, Frisch M (2009) Selection strategies for the development of rye introgression libraries. Theor Appl Genet 119:595–603PubMedGoogle Scholar
  47. Fletcher RS, Jack LM, Seth Y, Bauerle WL, Reuning G, Sen S, Eli M, Juenger TE, McKay JK (2013) Development of a next-generation NIL library in Arabidopsis thaliana for dissecting complex traits. Genomics 14:655PubMedGoogle Scholar
  48. Fonceka D, Tossim H-A, Rivallan R, Vignes H, Lacut E et al (2012) Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology. PLoS ONE 7:11Google Scholar
  49. Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2:a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88PubMedGoogle Scholar
  50. Fridman E, Carrari F, Liu YS, Fernie A, Zamir D (2004) Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science 305:1786–1789PubMedGoogle Scholar
  51. Fu Y, Yuan DD, Hu WJ, Cai CP, Guo WZ (2013) Development of Gossypium barbadense chromosome 18 segment substitution lines in the genetic standard line TM-1 of Gossypium hirsutum and mapping of QTLs related to agronomic traits. Acta Agron Sin 39:21–28Google Scholar
  52. Fukuda A, Shiratsuchi H, Fukushima A, Yamaguchi H, Mochida H, Terao T, Ogiwara H (2012) Detection of chromosomal regions affecting iron concentration in rice shoots subjected to excess ferrous iron using chromosomal segment substitution lines between japonica and indica. Plant Prod Sci 7:183–191Google Scholar
  53. Fukuda A, Sugimoto K, Ando T, YamamotoT Yano M (2014) Chromosomal locations of a gene underlying heat-accelerated brown spot formation and its suppressor genes in rice. Mol Genet Genomics. CrossRefPubMedGoogle Scholar
  54. Fukuoka S, Nonoue Y, Yano M (2010) Germplasm enhancement by developing advanced plant materials from diverse rice accessions. Breed Sci 60:509–517Google Scholar
  55. Furuta T, Uehara K, Angeles-Shim RB, Shim J, Ashikari M, Takashi T (2014) Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L. Breed Sci 63:468–475PubMedPubMedCentralGoogle Scholar
  56. Furuta T, Komeda N, Asano K, Uehara K, Gamuyao R, Shim R, Nagai K, Doi K et al (2015) Convergent loss of awn in two cultivated rice species Oryza sativa and Oryza glaberrima is caused by mutations in different loci. Genes Gen Genet 5:2267–2274Google Scholar
  57. Ghesquire A, Squier J, Second G, Lorieux M (1997) First steps towards a rational use of African rice, Oryza glaberrima, in rice breeding through a ‘contig line’ concept. Euphytica 96:31–39Google Scholar
  58. Gichuhi E, Him E, Takahashi H, Zhu S, Doi K, Tsugane K, Maekawa M (2016) Identification of QTLs for yield-related traits in RILs derived from the cross between pLIA-1 carrying Oryza longistaminata chromosome segments and Norin 18 in rice. Breed Sci 66:720–733PubMedPubMedCentralGoogle Scholar
  59. Goulet BE, Roda F, Hopkins R (2017) Hybridization in plants: old ideas, new techniques. Plant Physiol 173:65–78PubMedGoogle Scholar
  60. Gu L, Wei B, Fan R, Jia X, Wang X, Zhang X (2015) Development, identification and utilization of introgression lines using Chinese endemic and synthetic wheat as donors. J Integr Plant Biol 8:688–697Google Scholar
  61. Guo S, Wei Y, Li X, Liu K, Huang F, Chen C, Gao G (2013) Development and identification of introgression lines from cross of Oryza sativa and Oryza minuta. Rice Sci 20:95–102Google Scholar
  62. Guo Y, Guo X, Wang F, Wei Z, Zhang S, Wang L, Yuan Y, Zeng W, Zhang G, Zhang T, Song X, Sun X (2014) Molecular tagging and marker-assisted selection of fiber quality traits using chromosome segment introgression lines (CSILs) in cotton. Euphytica 200:239–250Google Scholar
  63. Guo L, Shi Y, Gong J, Liu A, Tan Y, Gong W, Li J, Chen T, Shang H, Ge Q, Lu Q, Sun J, Yuan Y (2018) Genetic analysis of the fiber quality and yield traits in G. hirsutum background using chromosome segments substitution lines (CSSLs) from Gossypium barbadense. Euphytica 214:82. Google Scholar
  64. Gupta M, Mason AS, Batley J, Bhartil S, Banga S, Banga S (2016) Molecular cytogenetic characterization of C-genome chromosome substitution lines in Brassica juncea (L.) Czern and Coss. Theor Appl Genet. CrossRefPubMedGoogle Scholar
  65. Gutierrez AG, Carabali SJ, Giraldo OX, Martinez CP, Correa F, Prado G, Tohme J, Lorieux M (2010) Identification of a rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa x O. glaberrima introgression lines. BMC Plant Biol 10:6PubMedPubMedCentralGoogle Scholar
  66. Gyenis L, Yun SJ, Smith KP, Steffenson BJ, Bossolini E, Muehlbauer GJ (2007) Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross. Genome 50:714–723PubMedGoogle Scholar
  67. Hao W, Jin J, Sun SY, Zhu MZ, Lin HX (2006) Construction of chromosome segment substitution lines carrying overlapping chromosome segments of the whole wild rice genome and identification of quantitative trait loci for rice quality. J Plant Physiol Mol Biol 32:354–362Google Scholar
  68. Hao W, Zhu MZ, Gao JP, Sun SY, Lin HX (2009) Identification of quantitative trait loci for rice quality in a population of chromosome segment substitution lines. J Integr Plant Biol 51:500–512PubMedGoogle Scholar
  69. Harlan JR (1976) Genetic resources in wild relatives of crops. Crop Sci 16:329–333Google Scholar
  70. Harper J, Armstead I, ThomasA James C, Gasior D, Bisaga M, Roberts L, King I, King J (2011) Alien introgression in the grasses Lolium perenne (perennial ryegrass) and Festuca pratensis (meadow fescue): the development of seven monosomic substitution lines and their molecular and cytological characterization. Ann Bot 107:1313–1321PubMedPubMedCentralGoogle Scholar
  71. Hashida Y, Aoki N, Kawanishi H, Okamura M, Ebitani T, Hirose T, Yamagishi T, Ohsugi R (2013) A near isogenic line of rice carrying chromosome segments containing OsSPS1 of Kasalath in the genetic background of Koshihikari produces an increased spikelet number per panicle. Field Crop Res 149:56–62Google Scholar
  72. He FH, Xi ZY, Zeng RZ, Tulukdar A, Zhang GQ (2005a) Developing single segment substitution lines (SSSLs) in rice (Oryza sativa L.) using advanced backcrosses and MAS. Acta Genetica Sin 32:825–883Google Scholar
  73. He FH, Xi ZY, Zeng RZ, Tulukdar A, Zhang GQ (2005b) Mapping of heading date QTLs in rice (Oryza sativa L.) using single segment substitution lines. Sci Agric Sin 38:1505–1513Google Scholar
  74. He FH, Xi ZY, Zeng RZ, Tulukdar A, Zhang GQ (2005c) Identification of QTL for plant height and its components by using single segment substitution lines in rice (Oryza sativa L.). Rice Sci 12:151–156Google Scholar
  75. He N, Wu R, Pan X, Peng L, Sun K, Zou T et al (2017) Development and trait evaluation of chromosome single segment substitution lines of O. meridionalis in the background of O. sativa. Euphytica 213:281Google Scholar
  76. Holbrook CC, Stalker HT (2010) Peanut breeding and genetic resources. In: Janick J (ed) Plant breeding reviews. Wiley, Hoboken, pp 297–356Google Scholar
  77. Hori K, Sato K, Nankaku N, Takeda K (2005) QTL analysis in recombinant chromosome substitution lines and doubled haploid lines derived from a cross between Hordeum vulgare ssp. vulgare and Hordeum vulgare ssp. spontaneum. Mol Breed 16:295–311Google Scholar
  78. Hori K, Sugimoto K, Nonoue Y, Ono N, Matsuba K, Yamanouchi U, Abe A, Takeuchi Y, Yano M (2010) Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars. Theor Appl Genet 120:1547–1557PubMedPubMedCentralGoogle Scholar
  79. Howell PM, Marshall DF, Lydiate DJ (1996) Towards developing intervarietal substitution lines in Brassica napus using marker assisted selection. Genome 39:348–358PubMedGoogle Scholar
  80. Hu Z, Wang W, Wu Z, Sun C, Li M, Lu J, Fu B, Shi J, Xu J, Ruan J, Wei C, Li Z (2018) Novel sequences, structural variations and gene presence variations of Asian cultivated rice. Sci Data 5:180079. CrossRefPubMedPubMedCentralGoogle Scholar
  81. Huang Y, Wu J, Wang P, Lin Y, Fu C, Deng Z, Wang Q, Li Q, Chen R, Zhang M (2015) Characterization of chromosome inheritance of the intergeneric BC2 and BC3 progeny between Saccharum spp. and Erianthus arundinaceus. PLoS ONE 10(7):e0133722. CrossRefPubMedPubMedCentralGoogle Scholar
  82. Jacquemin J, Bhatia D, Singh K, Wing RA et al (2013) The international oryza map alignment project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Curr Opin Plant Biol 16:147–156PubMedGoogle Scholar
  83. Jena KK, Khush GS, Kochert G (1992) RFLP analysis of rice (Oryza sativa L.) introgression lines. Theor Appl Genet 84:608–616PubMedGoogle Scholar
  84. Jeuken MJW, Lindhout P (2004) The development of lettuce backcross inbred lines (BILs) for exploitation of the Lactuca saligna (wild lettuce) germplasm. Theor Appl Genet 109:394–401PubMedGoogle Scholar
  85. Jie C, Bughio H, Chen DZ, Liu G, Zheng K, Zhuang J (2006) Development of chromosomal segment substitution lines from a backcross recombinant inbred population of interspecific rice cross. Rice Sci 13:15–21Google Scholar
  86. Jing Z, Qu Y, Yu C, Pan D, Fan Z, Chen J, Li C (2010) QTL analysis of yield-related traits using an advanced backcross population derived from common wild rice (Oryza rufipogon L.). Mol Plant Breed 1:1–10Google Scholar
  87. Kaeppler SM (1997) Quantitative trait locus mapping using sets of near-isogenic lines: relative power comparisons and technical considerations. Theor Appl Genet 95:384–392Google Scholar
  88. Kanbe T, Sasaki H, Aoki N, Yamagishi T, Ebitani T, Yano M, Ohsugi R (2008) Identification of QTLs toward improvement of plant type in rice (Oryza sativa L.) using Koshihikari/Kasalath chromosome segment substitution lines and backcross progeny F2 population. Plant Prod Sci 11:447–456Google Scholar
  89. Kanbe T, Sasaki H, Aoki N, Yamagishi T, Ohsugi R (2009) The QTL analysis of RuBisCO in flag leaves and non-structural carbohydrates in leaf sheaths of rice using chromosome segment substitution lines and backcross progeny F2 populations. Plant Prod Sci 12:224–232Google Scholar
  90. Kanjoo V, Punyawaew K, Siangliw JL, Jearakongman S, Vanavichit A, Toojinda T (2012) Evaluation of agronomic traits in chromosome segment substitution lines of KDML105 containing drought tolerance QTL under drought stress. Rice Sci 19:117–124Google Scholar
  91. Keurentjes JJB, Bentsink L, Alonso-Blanco C, Hanhart CJ, De Blankestijn Vries H, Effgen S, Vreugdenhil D, Koornneef M (2007) Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population. Genetics 175:891–905PubMedPubMedCentralGoogle Scholar
  92. Kim S-M, Suh J-P, Lee C-K, Lee J-H, Kim Y-G, Jena KK (2014) QTL mapping and development of candidate gene derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Genet Genomics 289:333–343PubMedGoogle Scholar
  93. Koumproglou R, Wilkes TM, Townson P, Wang XY, Beynon J, Pooni HS, Newbury HJ, Kearsey MJ (2002) STAIRS: a new genetic resource for functional genomic studies of Arabidopsis. Plant J 31:355–364PubMedGoogle Scholar
  94. Kubo T, Yuko A, Keiko N, Tsunematsu H, Doi K, Yoshimura A (2002) Reciprocal chromosome segment substitution series derived from japonica and indica cross of rice (Oryza sativa L.). Breed Sci 52:319–325Google Scholar
  95. Kumari BR, Kolesnikova-Allen MA, Hash CT, Senthilvel S, Nepolean T, Kisho KPB, Riera-Lizarazu Oscar, Witcombe JR, Srivastava RK (2014) Development of a set of chromosome segment substitution lines in pearl millet [Pennisetum glaucum (L.) R Br]. Crop Sci 54:2175–2182Google Scholar
  96. Kuspira J, Unrau J (1957) Genetic analyses of certain characters in common wheat using whole chromosome substitution lines. Can J Plant Sci 37:300–326Google Scholar
  97. Lan M, Yang Z, Shi Y, Ge R, Li A, Zhang B, Li J, Shang H, Liu A, Wang T, Yuan Y (2011) Assessment of substitution lines and identification of QTL related to fiber yield and quality traits in BC4F2 and BC4F3 populations from G hirsutum x G barbadense. Sci Agric Sin 44:3086–3097Google Scholar
  98. Lee HS, Sasaki K, Higashitani A, Ahn SN, Sato T (2012) Mapping and characterization of quantitative trait loci for mesocotyl elongation in rice (Oryza sativa L.). Rice 5:13PubMedPubMedCentralGoogle Scholar
  99. Lee HS, Sasaki K, Kang J-W, SatoT Song W-Y, Ahn SN (2017) Mesocotyl elongation is essential for seedling emergence under deep-seeding condition in rice. Rice 10:32PubMedPubMedCentralGoogle Scholar
  100. Lei J, Zhu S, Shao C, Tang S, Huang R, Zhu C, Yan S (2018) Mapping quantitative trait loci for cold tolerance at the booting stage in rice by using chromosome segment substitution lines. Crop Pasture Sci. CrossRefGoogle Scholar
  101. Li ZK (2001) QTL mapping in rice: a few critical considerations. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. Science Publishers, New Delhi, pp 153–171Google Scholar
  102. Li J, Xiao J, Grandillo S, Jiang L, Wang Y, Deng Q, Yuan L, McCouch SR (2004) QTL detection for rice grain quality traits using an interspecific backcross population de-rived from cultivated Asian (O. sativa L) and African (O. glaberrima S.) rice. Genome 47:697–704PubMedGoogle Scholar
  103. Li ZK, Fu BY, Gao YM, Xu JL, Ali J, Lafitte HR, Jiang YZ, Rey JD, Vijaya Kumar CHM, Maghirang R, Zheng TQ, Zhu LH (2005) Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Plant Mol Biol 59:33–52PubMedGoogle Scholar
  104. Li M, Sun P, Zhou H, Chen S, Yu S (2011) Identification of quantitative trait loci associated with germination using chromosome segment substitution lines of rice (Oryza sativa L.). Theor Appl Genet 123:411–420PubMedGoogle Scholar
  105. Li F, Jia HT, Liu L, Zhang CX, Liu ZJ, Zhang ZX (2014) Quantitative trait loci mapping for kernel row number using chromosome segment substitution lines in maize. Genet Mol Res 13:1707–1716PubMedGoogle Scholar
  106. Li X, Wang W, Wang Z, Li K, Lim YP, Piao Z (2015) Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa. Front Plant Sci 6:432. CrossRefPubMedPubMedCentralGoogle Scholar
  107. Li B, Shi Y, Gong J, Li J, Liu A, Shang H et al (2016) Genetic effects and heterosis of yield and yield component traits based on Gossypium barbadense chromosome segment substitution lines in two Gossypium hirsutum backgrounds. PLoS ONE 11(6):e0157978PubMedPubMedCentralGoogle Scholar
  108. Li P, Wang M, Lu Q, Ge Q, Rashid M, Liu A, Gong J (2017) Comparative transcriptome analysis of cotton fiber development of upland cotton (Gossypium hirsutum) and chromosome segment substitution lines from G. hirsutum × G. barbadense. BMC Genom 18:705Google Scholar
  109. Lin HX, Yamamoto T, Sasaki T, Yano M (2000) Characterization and detection of epistatic interactions of three QTLs, Hd1, Hd2 and Hd3 controlling heading date in rice using nearly isogenic lines. Theor Appl Genet 101:1021–1028Google Scholar
  110. Lin J, Zhu W, Zhang Y, Zhu Z, Zhao L, Chen T, Zhao Q, Zhou L, Fang Y, Wang C (2011) Detection of QTL for cold tolerance at bud bursting stage using chromosome segment substitution lines in rice (Oryza sativa). Rice Sci 18:71–74Google Scholar
  111. Lin XJ, Xu XW, Qian HM, Qi XH, Xu Q, Chen XH (2012) Analysis of cucumber chromosome segment introgression lines with powdery mildew resistance based on SSR markers. Acta Hort Sin 39:485–492Google Scholar
  112. Lippman ZB, Zamir D (2007) Heterosis: revisiting the magic. Trends Genet 23:60–66PubMedGoogle Scholar
  113. Liu S, Zhou R, Dong Y, Li P, Jia J (2006) Development, utilization of introgression lines using a synthetic wheat as donor. Theor Appl Genet 112:1360–1373PubMedGoogle Scholar
  114. Liu X, Wan X, Ma X, Wan J (2011) Dissecting the genetic basis for the effect of rice chalkiness, amylose content, protein content, and rapid viscosity analyzer profile characteristics on the eating quality of cooked rice using the chromosome segment substitution line population across eight environments. Genome 54:64–80PubMedGoogle Scholar
  115. Liu X, Sun X, Wang WY, Ding HF, Liu W, Li GX et al (2012) Fine mapping of Pa-6 gene for purple apiculus in rice. J Plant Biol 55:218–225Google Scholar
  116. Liu Q, Qin J, Li T, Liu E, Fan D, Edzesi WM et al (2015) Fine mapping and candidate gene analysis of qSTL3, a stigma length-conditioning locus in rice (Oryza sativa L.). PLoS ONE 10:e0127938. CrossRefPubMedPubMedCentralGoogle Scholar
  117. Liu W, Li X, Zhou K, Pan X, Li Y, Lu T, Shen X (2016) Mapping of QTLs controlling grain shape and populations construction derived from related residual heterozygous lines in rice. J Agric Sci 8:104–114Google Scholar
  118. Liu D, Yan Y, Fujita Y, Xu D (2018) Identification and validation of QTLs for 100-seed weight using chromosome segment substitution lines in soybean. Breed Sci Preview. CrossRefGoogle Scholar
  119. Lu MY, Li XH, Shang AL, Wang YM, Xi ZY (2011) Characterization of a set of chromosome single-segment substitution lines derived from two sequenced elite Maize inbred lines. Maydica 56:399–407Google Scholar
  120. Luo JJ, Hao W, Jin J, Gao JP, Lin HX (2008) Fine mapping of Spr3, a locus for spreading panicle from African cultivated rice (Oryza glaberrima Steud.). Mol Plant 1(5):830–838PubMedGoogle Scholar
  121. Ma X, Fu Y, Zhao X, Jiang L, Zhu Z, Gu P et al (2016) Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield associated QTLs using whole genome resequencing. Sci Rep 6:27425PubMedPubMedCentralGoogle Scholar
  122. Malathi S, Divya B, Sukumar M, Krishnam Raju A, Venkateswara Rao Y, Tripura Venkata VGN, Sarla N (2017) Identification of major effect QTLs for agronomic traits and CSSLs in rice from Swarna/O. nivara derived backcross inbred lines. Front Plant Sci 8:1027. CrossRefGoogle Scholar
  123. Mano Y, Omori F (2013) Flooding tolerance in interspecific introgression lines containing chromosome segments from teosinte (Zea nicaraguensis) in maize (Zea mays subsp mays). Ann Bot 112:1125–1139PubMedPubMedCentralGoogle Scholar
  124. Marzougui S, Sugimoto K, Yamanouchi U, Shimono M, Hoshino T, Hori K, Kobayashi M, Ishiyama K, Yano M (2012) Mapping and characterization of seed dormancy QTLs using chromosome segment substitution lines in rice. Theor Appl Genet 124:893–902PubMedGoogle Scholar
  125. Matus I, Corey A, Filichkin T, Hayes PM, Vales MI, Kling J, Riera-Lizarazu O, Sato K, Powell W, Waugh R (2003) Development and characterization of recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp spontaneum as a source of donor alleles in a Hordeum vulgare subsp vulgare background. Genome 46:1010–1023PubMedGoogle Scholar
  126. McCouch SR, Sweeney M, Li J, Jiang H, Thomson M, Septiningsih E, Edwards J, Moncada P, Xiao J, Garris A, Tai T, Martinez C, Tohme J, Sugiono M, Mcclung A, Yuan LP, Ahn SN (2007) Through the genetic bottleneck: O. rufipogon as a source of trait-enhancing alleles for O. sativa. Euphytica 154:317–339Google Scholar
  127. McCouch S, Wright M, Tung C-W, Maron L, McNally K, Fitzgerald M, Singh N, DeClerck G, Agosto Perez F, Korniliev P, Greenberg A, Nareda ME, Mercado SM, Harrington S, Shi Y, Branchini D, Kuser-Falçao LH, Ebana K, Yano M, Eizenga G, McClung A, Mezey J (2016) Open access resources for genome wide association mapping in rice. Nat Commun 7:10532PubMedPubMedCentralGoogle Scholar
  128. Mendez AM, Castillo D, del Pozo A, Matus I, Morcuende M (2011) Differences in stem soluble carbohydrate contents among recombinant chromosome substitution lines (RCSLs) of barley under drought in a Mediterranean-type environment. Agron Res 9:433–438Google Scholar
  129. Millet E, Rong JK, Qualset C, McGuire P, Bernard M, Sourdille P, Feldman M (2012) Production of chromosome-arm substitution lines of wild emmer in common wheat. Euphytica 190:1–17Google Scholar
  130. Monforte AJ, Tanksley SD (2000) Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L esculentum genetic background: a tool for gene mapping and gene discovery. Genome 43:803–813PubMedGoogle Scholar
  131. Mulsanti IW, Yamamoto T, Ueda T, Samadi AF, Kamahora E, Rumanti IA, Thanh VC, Adachi S, Suzuki S, Kanekatsu M, Hirasawa T, Ookawa T (2018) Finding the superior allele of japonica-type for increasing stem lodging resistance in indica rice varieties using chromosome segment substitution lines. Rice 11:25. CrossRefPubMedPubMedCentralGoogle Scholar
  132. Nadeau JH, Singer JB, Matin A, Lander ES (2000) Analysing complex genetic traits with chromosome substitution strains. Nat Genet 24:221–225PubMedGoogle Scholar
  133. Nakano H, Takai T, Kondo M (2018) Quantitative trait loci regulate the concentrations of steryl ferulates in brown rice. Cereal Chem. CrossRefGoogle Scholar
  134. Niones JM, Inukai Y, Suralta RR, Yamauchi A (2015) QTL associated with lateral root plasticity in response to soil moisture fluctuation stress in rice. Plant Soil 1:13Google Scholar
  135. Nounjan N, Siangliw J-L, Toojinda T, Chadchawan S, Theerakulpisut P (2016) Salt-responsive mechanisms in chromosome segment substitution lines of rice (Oryza sativa L. cv KDML105). Plant Phy Biochem 103:96–105Google Scholar
  136. Nounjan N, Chansongkrow P, Charoensawan V, Siangliw JL, Toojinda T, Chadchawan S, Theerakulpisut P (2018) High performance of photosynthesis and osmotic adjustment are associated with salt tolerance ability in rice carrying drought tolerance QTL: physiological and co-expression network analysis. Front Plant Sci 9:1135PubMedPubMedCentralGoogle Scholar
  137. Ogawa S, Valencia MO, Lorieux M, Arbelaez JD, McCouch S, Ishitani M, Selvaraj MG (2016) Identification of QTLs associated with agronomic performance under nitrogen-deficient conditions using chromosome segment substitution lines of a wild rice relative, Oryza rufipogon. Acta Physiol Plant 38:103. CrossRefGoogle Scholar
  138. Ookawa T, Aoba R, Yamamoto T, Ueda T, Takai T, Fukuoka S et al (2016) Precise estimation of genomic regions controlling lodging resistance using a set of reciprocal chromosome segment substitution lines in rice. Sci Rep 28:30572Google Scholar
  139. Orjuela J, Andrea G, Matthieu B, Arbelaez JD, Moreno L, Kimball J, Wilson G, Rami J, Joe T, McCouch SR, Lorieux M (2010) A universal core genetic map for rice. Theor Appl Genet 120:563–572PubMedGoogle Scholar
  140. Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang CX, Katsar CS, Lan TH, Lin YR, Ming R, Wright RJ (2000) Comparative genomics of plant chromosomes. Plant Cell 12:1523–1540PubMedPubMedCentralGoogle Scholar
  141. Peng X, He H, Zhu G, Jiang L, ZhuC YuQ, He J, Shen X, Yan S, Bian J (2017) Identification and analyses of chromosome segments affecting heterosis using chromosome-segment substitution lines in rice. Crop Sci 57:1836–1843Google Scholar
  142. Perez-Fons L, Wells T, Corol DI, Ward JL, Gerrish C, Beale MH et al (2014) A genome-wide metabolomic resource for tomato fruit from Solanum pennellii. Sci Rep 4:3859PubMedPubMedCentralGoogle Scholar
  143. Pestsova E, Borner A, Roder MS (2001) Development of a set of Triticum aestivumAegilops tauschii introgression lines. Hereditas 135:139–143PubMedGoogle Scholar
  144. Pestsova E, Borner A, Roder MS (2006) Development and QTL assessment of Triticum aestivumAegilops tauschii introgression lines. Theor Appl Genet 112:634–647PubMedGoogle Scholar
  145. Pillen K, Zacharias A, Leon J (2003) Advanced backcross QTL analysis in barley (Hordeum vulgare L.). Theor Appl Genet 107:340–352PubMedGoogle Scholar
  146. Pinson SRM, Liu G, Jia MH, Jia Y, Fjellstrom RG, Sharma A, Wang Y, Tabien RE, Li ZK (2012) Registration of a rice gene mapping population consisting of ‘TeQing’-into-‘Lemont’ (TIL) backcross introgression lines. J Plant Reg 6:128–135Google Scholar
  147. Pozo AD, Castillo D, Inostroza L, Matus I, Mendez AM, Morcuende R (2012) Physiological and yield responses of recombinant chromosome substitution lines of barley to terminal drought in a Mediterranean-type environment. Ann Appl Biol 160:157–167Google Scholar
  148. Puram VRR, Ontoy J, Linscombe S, Subudhi PK (2017) Genetic dissection of seedling stage salinity tolerance in rice using introgression lines of a salt tolerant landrace Nona Bokra. J Hered 108(6):658–670PubMedGoogle Scholar
  149. Qiao W, Qi L, Cheng Z, Su L, Li J, Sun Y et al (2016) Development and characterization of chromosome segment substitution lines derived from Oryza rufipogon in the genetic background of O. sativa spp indica cultivar 93-11. BMC Genom 17:580. CrossRefGoogle Scholar
  150. Qiu X, Chen K, Lv W, Ou X, Zhu Y, Xing D, Yang L, Fan F, Yang J, Xu J, Zheng T, Li Z (2017) Examining two sets of introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice (Oryza sativa L.). Theor Appl Genet 130(5):951–967. CrossRefPubMedPubMedCentralGoogle Scholar
  151. R Development Core Team (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing. ISBN 3-900051-07-0.
  152. Rahman H, ZhangY Sun L, Zhang K, Rahman S, Wu W, Zhan X, Cao L, Cheng S (2017) Genetic mapping of quantitative trait loci for the stigma exsertion rate in rice (Oryza sativa L). J Integr Agric 16(7):1423–1431Google Scholar
  153. Ramos JM, Furuta T, Uehara K, Chihiro N, Angeles-Shim RB, Shim J et al (2016) Development of chromosome segment substitution lines (CSSLs) of O longistaminata A Chev & Rohr in the background of the elite japonica rice cultivar, Taichung 65 and their evaluation for yield traits. Euphytica 210:151–163Google Scholar
  154. Ramsay LD, Jennings DE, Bohuon EJR, Arthur AE, Lydiate DJ, Kearsey MJ, Marshall DF (1996) The construction of a substitution library of recombinant backcross lines in Brassica oleracea for the precision mapping of quantitative trait loci. Genome 39:558–567PubMedGoogle Scholar
  155. Rangel PN, Brondani RPV, Rangel PHN, Brondani C (2008) Agronomic and molecular characterization of introgression lines from the interspecific cross O. sativa BG90-2 x Oryza glumaepatula RS-16. Genet Mol Res 7:184–195PubMedGoogle Scholar
  156. Ren D, Rao Y, Huang L, Leng Y, Hu J, Lu M et al (2016) Fine mapping identifies a new QTL for brown rice rate in rice (Oryza sativa L.). Rice 9:4PubMedPubMedCentralGoogle Scholar
  157. Ronen G, Goren LC, Zamir D, Hirschberg J (2000) An alternative pathway to β-carotene formation in plant chromoplasts discovered by map-based cloning of Beta and old-gold color mutations in tomato. Proc Natl Acad Sci USA 97(20):11102–11107PubMedGoogle Scholar
  158. Rousseaux MC, Jones CM, Adams D, Chetelat R, Bennett A, Powell A (2005) QTL analysis of fruit antioxidants in tomato using Lycopersicon pennellii introgression lines. Theor Appl Genet 111:1396–1408PubMedGoogle Scholar
  159. Ruggieri V, Sacco A, Calafiore R, Frusciante L, Barone A (2015) Dissecting a QTL into candidate genes highlighted the key role of pectin esterases in regulating the ascorbic acid content in tomato fruit. Plant Genome 8(2):1–10. CrossRefGoogle Scholar
  160. Saha S, Stelly DM, Raska DA, Wu J, Jenkins JN, McCarty JC et al (2012) Chromosome substitution lines: concept, development and utilization in the genetic improvement of upland cotton. In: Abdurakhmonov IY (ed) Plant breeding. InTech Press, Rijeka, pp 107–128. CrossRefGoogle Scholar
  161. Salvi S, Corneti S, Bellotti M, Carraro N, Sanguineti MC, Castelletti S, Tuberosa R (2011) Genetic dissection of maize phenology using an intraspecific introgression library. BMC Plant Biol 11:4. CrossRefPubMedPubMedCentralGoogle Scholar
  162. Sasaki K, Takeuchi Y, Miura K, Yamaguchi T, Ando T, Ebitani T, Higashitani A, Yamaya T, Yano M, Sato T (2015) Fine mapping of a major quantitative trait locus, qLG-9, that controls seed longevity in rice (Oryza sativa L.). Theor Appl Genet 128:769–778PubMedGoogle Scholar
  163. Sato K, Takeda K (2009) An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines. Theor Appl Genet 119:613–619PubMedGoogle Scholar
  164. Sato K, Close TJ, Bhat P, Muñoz-Amatriaín M, Muehlbauer GJ (2011) Single nucleotide polymorphism mapping and alignment of recombinant chromosome substitution lines in barley. Plant Cell Physiol 52:728–737PubMedGoogle Scholar
  165. Schauer N, Semel Y, Roessner U et al (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24:447–454PubMedGoogle Scholar
  166. Schmalenbach I, Pillen K (2009) Detection and verification of malting quality QTLs using wild barley introgression lines. Theor Appl Genet 118:1411–1427PubMedPubMedCentralGoogle Scholar
  167. Schmalenbach I, Korber N, Pillen K (2008) Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust. Theor Appl Genet 117:1093–1106PubMedGoogle Scholar
  168. Schmalenbach I, Leon J, Pillen K (2009) Identification and verification of QTLs for agronomic traits using wild barley introgression lines. Theor Appl Genet 118:483–497PubMedGoogle Scholar
  169. Semel Y, Nissenbaum J, Menda N, Zinder M, Krieger U, Issman N, Pleban T, Lippman Z, Gur A, Zamir D (2006) Overdominant quantitative trait loci for yield and fitness in tomato. Proc Natl Acad Sci USA 103:12981–12986PubMedGoogle Scholar
  170. Shan JX, Zhu MZ, Shi M, Gao JP, Lin HX (2009) Fine mapping and candidate gene analysis of spd6, responsible for small panicle and dwarfness in wild rice (Oryza rufipogon Griff). Theor Appl Genet 119:827–836PubMedGoogle Scholar
  171. Sharma S, Upadhyaya HD, Varshney RK, Gowda CLL (2013) Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes. Front Plant Sci 4:309. CrossRefPubMedPubMedCentralGoogle Scholar
  172. Shen G, Xing Y (2014) Two novel QTLs for heading date are identified using a set of chromosome segment substitution lines in rice (Oryza sativa L.). J Genet Genomics 41:659–662PubMedGoogle Scholar
  173. Shen YY, Liu LL, Jiang L, Zhang YX, Wan JM (2011) Detection of stably-expressed QTL for rice fat content using BIL and CSSL populations. Rice Genet Newsl 24:71–73Google Scholar
  174. Shen G, Zhan W, Chen H, Xing Y (2014) Dominance and epistasis are the main contributors to heterosis for plant height in rice. Plant Sci 215:11–18PubMedGoogle Scholar
  175. Shim RA, Angeles ER, Ashikari M, Takashi T (2010) Development and evaluation of Oryza glaberrima Steud chromosome segment substitution lines (CSSLs) in the background of O. sativa L. Cv Koshihikari. Breed Sci 60:613–619Google Scholar
  176. Simpson CE (2001) Use of wild Arachis species: introgression of genes into A. hypogaea L. peanut. Science 28:114–116Google Scholar
  177. Singh N, Choudhury DR, Singh AK, Kumar S, Srinivasan K, Tyagi RK, Singh NK, Singh R et al (2013) Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties. PLoS ONE 8(12):e84136. CrossRefPubMedPubMedCentralGoogle Scholar
  178. Singh N, Jayaswal PK, Panda K, Mandal P, Kumar V, Singh B, Mishra S, Singh Y, Singh R, Rai V, Gupta A, Sharma TR, Singh NK (2015) Single copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice. Sci Rep 5:11600PubMedPubMedCentralGoogle Scholar
  179. Singh R, Singh Y, Xalaxo S, Verulkar S, Yadav N, Singh S et al (2016) From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network. Plant Sci 242:278–287PubMedGoogle Scholar
  180. Sobrizal KI, Sanchez PL, Doi K, Angeles ER, Khush GS, Yoshimura A (1999) Development of Oryza glumaepatula introgression lines in rice, O. sativa L. Rice Gene Nlet 16:107–108Google Scholar
  181. Subudhi PK, De Leon T, Singh PK, Parco A, Cohn MA, Sasaki T (2015) A chromosome segment substitution library of weedy rice for genetic dissection of complex agronomic and domestication traits. PLoS ONE 10:e0130650. CrossRefPubMedPubMedCentralGoogle Scholar
  182. Suralta RR, Inukai Y, Yamauchi A (2008) Utilizing chromosome segment substitution lines (CSSLs) for evaluation of root responses to transient moisture stresses in rice. Plant Prod Sci 11(4):457–465Google Scholar
  183. Svabova L, Aubert G, Smykal P (2016) Wild pea Pisum fulvum and Pisum elatius chromosome segment substitution lines in cultivated P. sativum genetic background. In: International legume society conference—legumes for a sustainable world, Oct 2016, Lisbon, Portugal, p 358Google Scholar
  184. Swamy BPM, Sarla N (2008) Yield-enhancing quantitative trait loci (QTLs) from wild species. Biotech Adv 26:106–120Google Scholar
  185. Szalma SJ, Hostert BM, Ledeaux JR, Stuber CW et al (2007) QTL mapping with near-isogenic lines in maize. Theor Appl Genet 114:1211–1228PubMedGoogle Scholar
  186. Taguchi-Shiobara F, Ozaki H, Sato H, Maeda H, Kojima Y, Ebitani T, Yano M (2013) Mapping and validation of QTLs for rice sheath blight resistance. Breed Sci 63:301–308PubMedPubMedCentralGoogle Scholar
  187. Takai T, Nonoue Y, Yamamoto S, Yamanouchi U, Matsubara K, Liang ZW, Lin H, Ono N, Uga Y, Yano M (2007) Development of chromosome segment substitution lines derived from backcross between indica donor rice cultivar ‘Nona Bokra’ and japonica recipient cultivar Koshihikari. Breed Sci 57:257–261Google Scholar
  188. Takai T, Ikka T, Kondo K, Nonoue Y, Ono N, Arai-Sanoh Y, Yoshinaga S, Nakano H, Yano M, Kondo M, Yamamoto T (2014) Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines. BMC Plant Biol 14:295–306PubMedPubMedCentralGoogle Scholar
  189. Takayuki K (2014) Identification of quantitative trait loci for resistance to bending-type lodging in rice (Oryza sativa L.). Euphytica 198:353–367Google Scholar
  190. Tang ZX, Xiao J, Hu WM, Yu B, Xu CW (2012) Bin-based model construction and analytical strategies for dissecting complex traits with chromosome segment substitution lines. Chin Sci Bull 57:2666–2674Google Scholar
  191. Tao Y, Zhu J, Xu J, Wang L, Gu H, Zhou R, Yang Z, ZhouY Liang G (2016) Exploitation of heterosis loci for yield and yield components in rice using chromosome segment substitution lines. Sci Rep 6:36802. CrossRefPubMedPubMedCentralGoogle Scholar
  192. Tazib T, Kobayashi Y, Koyama H, Matsui T (2015) QTL analyses for anther length and dehiscence at flowering as traits for the tolerance of extreme temperatures in rice (Oryza sativa L.). Euphytica 1:14Google Scholar
  193. Thomson J, Singh N, Dwiyanti MS, Wang DR, Wright MH, Perez FA, DeClerk G et al (2017) Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications. Rice 10:40PubMedPubMedCentralGoogle Scholar
  194. Tian F, Li DJ, Fu Q, Zhu ZF, Fu YC, Wang XK, Sun CQ (2006) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580PubMedGoogle Scholar
  195. Tian FK, Ruan BP, Yan MX, Ye SF, Peng YL, Dong GJ, Zhu L, Hu J, Yan HL, Guo LB, Qian Q, Gao ZY (2013) Genetic analysis and QTL mapping of mature seed culturability in indica rice. Rice Sci 20:313–329Google Scholar
  196. Torjek O, Meyer RC, Zehnsdorf M, Teltow M, Strompen G, WituckaWall H, Blacha A, Altmann T (2008) Construction and analysis of 2 reciprocal Arabidopsis introgression line populations. J Hered 99:396–406PubMedGoogle Scholar
  197. Tung CW, Zhao K, Wright M, Ali ML, Jung J, Kimball J, Tyagi W, Thomson MJ, McNally K, Leung H, Kim H, Ahn SN, Reynolds A, Scheffle B, Eizenga G, McClung A, Bustamante C, McCouch SR (2010) Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.). Rice 3:205–217Google Scholar
  198. Uehara K, Furuta T, Masuda K, Yamada S, Angeles-Shim RB, Ashikari M, Takashi T (2017) Construction of rice chromosome segment substitution lines harbouring Oryza barthii genome and evaluation of yield-related traits. Breed Sci Preview. CrossRefGoogle Scholar
  199. Uga Y, Kitomi Y, Yamamoto E, Kanno N, Kawai S, Mizubayashi T, Fukuoka S (2015) A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of deeper rooting. Rice 8:8PubMedPubMedCentralGoogle Scholar
  200. Ujiie K, Ishimaru K (2014) Alleles affecting 30 traits for productivity in two japonica Rice varieties, Koshihikari and Nipponbare (Oryza sativa L.). Plant Prod Sci 17:47–65Google Scholar
  201. Ujiie K, Kashiwagi T, Ishimaru K (2012) Identification and functional analysis of alleles for productivity in two sets of chromosome segment substitution lines of rice. Euphytica 187:325–337Google Scholar
  202. Ujiie K, Toshio Y, Masahiro Y, Ken I (2016) Genetic factors determining varietal differences in characters affecting yield between two rice (Oryza sativa L.) varieties, Koshihikari and IR64. Genet Resour Crop Evol 63:97–123Google Scholar
  203. Ulloa M, Wang C, Saha S, Hutmacher RB, Stelly DM, Jenkins JN, Burke J, Roberts PA (2016) Analysis of root-knot nematode and fusarium wilt disease resistance in cotton (Gossypium spp.) using chromosome substitution lines from two alien species. Genetica 144:167–179PubMedGoogle Scholar
  204. van Berloo R (2008) GGT 20: versatile software for visualization and analysis of genetic data. J Hered 99:232–236PubMedGoogle Scholar
  205. Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27(9):522–530PubMedGoogle Scholar
  206. Varshney RK, Terauchi R, McCouch SR (2014) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12(6):e1001883. CrossRefPubMedPubMedCentralGoogle Scholar
  207. von Korff M, Wang H, Leon J, Pillen K (2004) Development of candidate introgression lines using an exotic barley accession (Hordeum vulgare ssp. spontaneum) as donor. Theor Appl Genet 109:1736–1745Google Scholar
  208. von Korff M, Wang H, Leon J, Pillen K (2005) AB-QTL analysis in spring barley I Detection of resistance genes against powdery mildew, leaf rust and scald introgressed from wild barley. Theor Appl Genet 111:583–590Google Scholar
  209. von Korff M, Wang H, Leon J, Pillen K (2006) AB-QTL analysis in spring barley: II Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H vulgare ssp spontaneum). Theor Appl Genet 112:1221–1231Google Scholar
  210. Wan XY, Wan JM, Su CC, Wang CM, Shen WB, Li JM, Wang HL et al (2004) QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines. Theor Appl Genet 110:71–79PubMedGoogle Scholar
  211. Wan XY, Wan JM, Jiang L, Wang JK, Zhai HQ, Weng JF, Wang HL, Lei CL, Wang JL, Zhang X, Cheng ZJ, Guo XP (2006) QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects. Theor Appl Genet 112:1258–1270PubMedGoogle Scholar
  212. Wang X, Roy IL, Nicodeme E, Li R, Wangner R, Petros C et al (2003) Using advanced intercross lines for high-resolution mapping of HDL cholesterol quantitative trait loci. Genome Res 13:1654–1664PubMedPubMedCentralGoogle Scholar
  213. Wang J, Wan X, Crossa J, Crouch J, Weng J, Zhai H, Wan J (2006) QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines. Genet Res 88:93–104PubMedGoogle Scholar
  214. Wang LQ, Zhao YF, Xue YD, Zhang ZX, Zheng YL, Cheng JT (2007) Development and evaluation of two link-up single segment introgression lines (SSILs) in Zea mays. Acta Agron Sin 33:663–668Google Scholar
  215. Wang L, Yang A, He C, Qu M, Zhang J (2008) Creation of new maize germplasm using alien introgression from Zea mays ssp. Mexicana. Euphytica 164:789–801Google Scholar
  216. Wang P, Zhu Y, Song X, Cao Z, Ding Y, Liu B, Zhu X, Wang S, Guo W, Zhang T (2012a) Inheritance of long staple fiber quality traits of Gossypium barbadense in G hirsutum background using CSILs. Theor Appl Genet 124:1415–1428PubMedGoogle Scholar
  217. Wang Z, Yu C, Liu X, Liu S, Yin C, Liu L, Lei J, Jiang L, Yang C, Chen L et al (2012b) Identification of indica rice chromosome segments for the improvement of japonica inbreds and hybrids. Theor Appl Genet 124:1351–1364PubMedGoogle Scholar
  218. Wang W, He Q, Yang H, Xiang S, Zhao T, Gai J (2013) Development of a chromosome segment substitution line population with wild soybean (Glycine soja Sieb et Zucc) as donor parent. Euphytica 189:293–307Google Scholar
  219. Wang H, Zhang X, Yang H, Chen Y, Yuan L, Li W, Liu Z, Tang J, Kang D (2016) Heterotic loci identified for plant height and ear height using two CSSLs test populations in maize. J Integr Agric 15(12):2726–2735Google Scholar
  220. Wang Y, Jiang Q, Liu J, Zeng W, Zeng Y, Zeng Y, Li R, Luo J (2017) Comparative transcriptome profiling of chilling tolerant rice chromosome segment substitution line in response to early chilling stress. Genes Genom 39:127–141Google Scholar
  221. Wang Y, Zhang X, Shi X, Sun C, Jin J, Tian R, Wei X, Xie H, Guo Z, Tang J (2018) Heterotic loci identified for maize kernel traits in two chromosome segment substitution line test populations. Sci Rep 8:11101PubMedPubMedCentralGoogle Scholar
  222. Xi ZY, He FH, Zeng RZ, Zhang ZM, Ding XH, Li WT, Zhang GQ (2006) Development of a wide population of chromosome single-segment substitution lines in the genetic background of an elite cultivar of rice (Oryza sativa L.). Genome 49:476–484PubMedGoogle Scholar
  223. Xiao J, Liang Y, Li K, Zhou Y, Cai W, Zhou Y et al (2010) A novel strategy for genetic dissection of complex traits: the population of specific chromosome substitution strains from laboratory and wild mice. Mamm Genome 21(7–8):370–376PubMedGoogle Scholar
  224. Xie X, Chen Z, Cao J, Guan H, Lin D et al (2014) Towards the positional cloning of qBlsr5a, a QTL underlying resistance to bacterial leaf streak using overlapping sub-CSSLs in rice. PLoS ONE 9:e95751PubMedPubMedCentralGoogle Scholar
  225. Xin XY, Wang WX, Yang JS, Luo XJ (2011) Genetic analysis of heterotic loci detected in a cross between indica and japonica rice (Oryza sativa L.). Breed Sci 61:380–388PubMedPubMedCentralGoogle Scholar
  226. Xin D, Qi Z, Jiang H, Hu Z, Zhu R, Hu J et al (2016) QTL location and epistatic effect analysis of 100-seed weight using wild soybean (Glycine soja Sieb & Zucc) chromosome segment substitution lines. PLoS ONE 11(3):e0149380PubMedPubMedCentralGoogle Scholar
  227. Xu J, Zhao Q, Du P, Xu C, Wang B, Feng Q, Liu Q, Tang S, Gu M, Han B, Liang G (2010) Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genom 11:656Google Scholar
  228. Xu Q, Shi Y, Yu T, Xu X, Yan Y, Qi X, Chen X (2016) Whole-Genome resequencing of a cucumber chromosome segment substitution line and its recurrent parent to identify candidate genes governing powdery mildew resistance. PLoS ONE 11(10):e0164469PubMedPubMedCentralGoogle Scholar
  229. Xu Q, Xu X, Shi Y, Qi X, Chen X (2017) Elucidation of the molecular responses of a cucumber segment substitution line carrying Pm51 and its recurrent parent triggered by powdery mildew by comparative transcriptome profiling. BMC Genom 18:21Google Scholar
  230. Yamamoto T, Kuboki Y, Lin SY, Sasaki T, Yano M (1998) Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice as single Mendelian factors. Theor Appl Genet 97:37–44Google Scholar
  231. Yamamoto T, Yonemaru J, Yano M (2009) Towards the understanding of complex traits in rice: substantially or superficially? DNA Res 16:141–154PubMedPubMedCentralGoogle Scholar
  232. Yamanouchi U, Yano M, Lin H, Ashikari M, Yamada K (2002) A rice spotted leaf gene, Spl7, encodes a heat stress transcription factor protein. Proc Natl Acad Sci 99:7530–7535PubMedGoogle Scholar
  233. Yang Z, Li J, Li A, Zhang B, Liu G, Li J, Shi Y, Liu A, Jiang J, Wang T, Yuan Y (2009) Developing chromosome segment substitution lines (CSSLs) in cotton (Gossypium) using advanced backcross and MAS. Mol Plant Breed 2:233–241Google Scholar
  234. Yang D, Zhang Y, Zhu Z, Chen T, Zhao Q, Yao S, Zhao L, Lin J, Zhu W, Wang C (2013) Substitutional mapping the cooked rice elongation by using chromosome segment substitution lines in rice. Mol Plant Breed 13:107–115Google Scholar
  235. Yang Y, Xu J, Leng Y, Xiong G, Hu J, Zhang G, Huang L, Wang L et al (2014) Quantitative trait loci identification, fine mapping and gene expression profiling for ovicidal response to whitebacked planthopper (Sogatella furcifera Horvath) in rice (Oryza sativa L.). BMC Plant Biol 14:145PubMedPubMedCentralGoogle Scholar
  236. Yang Y, Guo M, Li R, Shen L, Wang W, Liu M, Zhu Q, Hu Z et al (2015) Identification of quantitative trait loci responsible for rice grain protein content using chromosome segment substitution lines and fine mapping of qPC-1 in rice (Oryza sativa L.). Mol Breed 35:130Google Scholar
  237. Yang D, Ye X, Zheng X, Cheng C, Ye N, Huang F (2016) Development and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of the whole wild rice genome. Front Plant Sci 7:1737. CrossRefPubMedPubMedCentralGoogle Scholar
  238. Yano M, Katayose Y, Ashikar M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod-sensitivity QTL in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2484PubMedPubMedCentralGoogle Scholar
  239. Yasui H, Yamagata Y, Yoshimura A (2010) Development of chromosomal segment substitution lines derived from indica rice donor cultivars DV85 and ARC10313 in the genetic background of japonica cultivar Taichung 65. Breed Sci 60:620–628Google Scholar
  240. Ye G, Liang S, Wan JM (2010) QTL mapping of protein content in rice using single chromosome segment substitution lines. Theor Appl Genet 121(4):741–750PubMedGoogle Scholar
  241. Ye W, Hu S, Wu L, Ge C, Cui Y, Chen P, Xu J, Dong G, Guo L, Qian Q (2017) Fine mapping a major QTL qFCC7L for chlorophyll content in rice (Oryza sativa L.) cv PA64s. Plant Growth Regul 81:81–90Google Scholar
  242. Yu CY, Wan JM, Zhai HQ, Wang CM, Jiang L, Xiao YH, Liu YQ (2005) Study on heterosis of inter-subspecies between indica and japonica rice (Oryza sativa L.) using chromosome segment substitution lines. Chin Sci Bull 50:131–136Google Scholar
  243. Yun SJ, Gyenis L, Bossolini E, Hayes PM, Matus I, Smith KP, Steffenson BJ, Tuberosa R, Muehlbauer GJ (2006) validation of quantitative trait loci for multiple disease resistance in barley using advanced backcross lines developed with a wild barley. Crop Sci 46:1179–1186Google Scholar
  244. Zhai H, Gong W, Tan Y, Liu A, Song W, Li J et al (2016) Identification of chromosome segment substitution lines of Gossypium barbadense introgressed in G hirsutum and quantitative trait locus mapping for fiber quality and yield traits. PLoS ONE 11(9):e0159101PubMedPubMedCentralGoogle Scholar
  245. Zhang W, Bin J, Chen L, Zheng L, Ji S, Xia Y (2008) QTL mapping for crude protein and protein fraction contents in rice (Oryza sativa L.). J Cereal Sci 48(2):539–547Google Scholar
  246. Zhang H, Zhao Q, Sun ZZ, Zhang CQ, Feng Q, Tang SZ, Liang GH, Gu MH, Han B, Liu QQ (2011) Development and high-throughput genotyping of substitution lines carrying the chromosome segments of indica 9311 in the background of japonica Nipponbare. J Genet Genomics 38:603–611PubMedGoogle Scholar
  247. Zhang J, Dan Y, Liang Y, Gu Y, Zhang B, Zhang B, Li J, Gong J, Liu A, Shang H, Wang T, Gong M, Yuan Y (2012) Evaluation of yield and fiber quality traits of chromosome segments substitution lines population (BC5F3 and BC5F3:4) in cotton. J Plant Genet Resour 13:773–781Google Scholar
  248. Zhang C, Hu B, Zhu K, Zhang H, Leng Y, Tang S, Gu M, Liu Q (2013) QTL mapping for rice RVA properties using high-throughput re-sequenced chromosome segment substitution lines. Rice Sci 20(6):407–414Google Scholar
  249. Zhang H, Lian D, Ji-Song D, Chang-Quan Z, Juan L, Ming-Hong G, Qiao-Quan L, Ying Z (2014) Major QTLs reduce the deleterious effects of high temperature on rice amylose content by increasing splicing efficiency of wx pre-mRNA. Theor Appl Genet 127:273–282PubMedGoogle Scholar
  250. Zhang S, Zhu X, Feng L, Gao X, Yang B, Zhang T, Zhou B-L (2016) Mapping of fiber quality QTLs reveals useful variation and footprints of cotton domestication using introgression lines. Sci Rep 6:31954PubMedPubMedCentralGoogle Scholar
  251. Zhang H, Mittal N, Leamy LJ, Barazani O, Song BH (2017) Back into the wild-Apply untapped genetic diversity of wild relatives for crop improvement. Evol Appl. CrossRefPubMedGoogle Scholar
  252. Zhao F-M, Liu G, Zhu H, Ding X, Zeng R, Zhang Z, Li W, Zhang G (2008) Unconditional and conditional QTL mapping for tiller numbers at various stages with Single Segment Substitution Lines in rice (Oryza sativa L.). Agric Sci China 7:257–265Google Scholar
  253. Zhao LN, Zhou HJ, Lu LX, Liu L, Li XH, Lin YJ, Yu SB (2009) Identification of quantitative trait loci controlling rice mature seed culturability using chromosomal segment substitution lines. Plant Cell Rep 28:247–256PubMedGoogle Scholar
  254. Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467PubMedPubMedCentralGoogle Scholar
  255. Zhao FM, Tan Y, Zheng LY, Zhou K, He GH, Ling YH, Zhang LH, Xu SZ (2016a) Identification of rice chromosome segment substitution line z322-1-10 and mapping QTLs for agronomic traits from the F3 population. Cereal Res Commun 44:370–380Google Scholar
  256. Zhao L, Lei J, Huang Y, Zhu S, Chen H, Huang R, Peng Z, Tu Q, Shen X, Yan S (2016b) Mapping quantitative trait loci for heat tolerance at anthesis in rice using chromosomal segment substitution lines. Breed Sci 66:358–366. CrossRefPubMedPubMedCentralGoogle Scholar
  257. Zhao C, Zhao Q, Zhao L, Zhou L, Chen T, Yao S, Liang W, Zhang Y, Wang C (2018) Characterization and fine mapping of qPE12, a new locus controlling rice panicle exsertion. Euphytica 214:47. CrossRefGoogle Scholar
  258. Zheng L, Zhang W, Liu S, Chen L, Liu X, Chena X, Ma J, Chen W, Zhao Z, Jiang L, Wan J (2012) Genetic relationship between grain chalkiness, protein content, and paste viscosity properties in a backcross inbred population of rice. J Cereal Sci 56:153–160Google Scholar
  259. Zheng JX, Zhang YX, Qin BX, Qiu YF et al (2014) Pyramiding and interacting effects of QTLs for cold tolerance at the seedling stage in common wild rice, Oryza rufipogon Griff. J S China Agric Univ 35(1):29–36Google Scholar
  260. Zhou L, Chen L, Jiang L, Zhang W, Liu L, Liu X, Zhao Z, Liu S, Zhang L, Wang J, Wan J (2009) Fine mapping of the grain chalkiness QTL qPGWC-7 in rice (Oryza sativa L.). Theor Appl Genet 118:581–590PubMedGoogle Scholar
  261. Zhou Y, Dong G, Tao Y, Chen C, Yang B, Wu Y, Yang Z, Liang G, Wang B, Wang Y (2016) Chromosome segment substitution lines derived from 9311 and Nipponbare in rice (Oryza sativa L.). PLoS ONE 11(3):e0151796. CrossRefPubMedPubMedCentralGoogle Scholar
  262. Zhou Y, Tao Y, Tang D, Wang J, Zhong J, Wang Y, Yuan Q, Yu X, Zhang Y, Wang Y, Liang G, Dong G (2017a) Identification of QTL associated with nitrogen uptake and nitrogen use efficiency using high throughput genotyped CSSLs in rice (Oryza sativa L.). Front Plant Sci 8:1166PubMedPubMedCentralGoogle Scholar
  263. Zhou Y, Xie Y, Cai J, Liu C, Zhu H, Jiang R, Zhong Y, Zhang G et al (2017b) Substitution mapping of QTLs controlling seed dormancy using single segment substitution lines derived from multiple cultivated rice donors in seven cropping seasons. Theor Appl Genet 130:1191. CrossRefPubMedGoogle Scholar
  264. Zhu WY, Lin J, Yang DW, Zhao L, Zhang YD, Zhu Z, Chen T, Wang CL (2009) Development of chromosome segment substitution lines derived from backcross between two sequenced rice cultivars, indica recipient 93-11 and japonica donor Nipponbare. Plant Mol Biol Rep 27:126–131Google Scholar
  265. Zhu YJ, Zuo SM, Chen ZX, Chen XG, Li G, Zhang YF, Zhang GQ, Pan XB (2014) Identification of two major rice sheath blight resistance QTLs, qSB1-1HJX74 and qSB11HJX74, in field trials using chromosome segment substitution lines. Plant Dis 98:1112–1121Google Scholar
  266. Zhu I, NiuY Tao Y, Wang J, Jian J, Tai S, Li J et al (2015) Construction of high-throughput genotyped chromosome segment substitution lines in rice (Oryza sativa L.) and QTL mapping for heading date. Plant Breed 134(2):156–163Google Scholar
  267. Zong G, Wang A, Wang L, Liang G, Gu M, Sang T, Han B (2012) A pyramid breeding of eight grain-yield related quantitative trait loci based on marker-assistant and phenotype selection in rice (Oryza sativa L.). J Genet Genom 39:335–350Google Scholar
  268. Zuo S, Zhang Y, Chen Z, Jiang W, Feng M, Pan XB (2014) Improvement of rice resistance to sheath blight by pyramiding QTLs conditioning disease resistance and tiller angle. Rice Sci 21:318–326Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Divya Balakrishnan
    • 1
  • Malathi Surapaneni
    • 1
  • Sukumar Mesapogu
    • 1
  • Sarla Neelamraju
    • 1
    Email author
  1. 1.ICAR- National Professor Project, ICAR- Indian Institute of Rice ResearchHyderabadIndia

Personalised recommendations