Abstract
Cultivated rice (Oryza sativa) originated from common wild rice (Oryza rufipogon) and inherited its advantages. However, during the rice domestication process, some valuable features of wild rice, such as tolerance to biotic and abiotic stress, were lost. To fully utilize wild rice germplasm resources, we constructed a set of introgression lines (ILs) using a common wild rice material from Lingshui, China. A set of high-resolution InDel molecular markers with an average interval of 2.39 Mb were designed to carry out marker-assisted selection and identification of segment characteristics. The ILs contained 77 lines including 1.286 introgressed fragments with an average length of 6.511 Mb, covering 93.59% of the donor parent’s chromosomes. The agricultural traits of 77 lines were investigated. Many old quantitative trait loci (QTLs) involved in plant height, awn length, seed traits and other characteristics reappeared in our ILs, proving that our system was reliable. Further, many new QTLs were identified. A QTL related to drought tolerance located on chromosome 4 was thoroughly elaborated. This set of ILs provides a new resource for utilizing the excellent features of wild rice.
Similar content being viewed by others
References
Asano K, Yamasaki M, Takuno S, Miura K, Katagiri S, Ito T, Doi K, Wu JZ, Ebana K, Matsumoto T, Innan H, Kitano H, Ashikari M, Matsuoka M (2011) Artificial selection for a green revolution gene during japonica rice domestication. Proc Natl Acad Sci USA 108:11034-11039
Bessho-Uehara K, Wang DR, Furuta T, Minami A, Nagai K, Gamuyao R, Asano K, Angeles-Shim RB, Shimizu Y, Ayano M, Komeda N, Doi K, Miura K, Toda Y, Kinoshita T, Okuda S, Higashiyama T, Nomoto M, Tada Y, Shinohara H, Matsubayashi Y, Greenberg A, Wu J, Yasui H, Yoshimura A, Mori H, McCouch SR, Ashikari M (2016) Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice. Proc Natl Acad Sci USA 113:8969-8974
Chen ML, Luo J, Shao GN, Wei XJ, Tang SQ, Sheng ZH, Song J, Hu PS (2012) Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1. Plant Cell Rep 31:863–872
Ding XP, Li XK, Xiong LZ (2011) Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice. Theor Appl Genet 123:815–826
Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321
Du B, Zhang WL, Liu BF, Hu J, Wei Z, Zy S, He RF, Zhu LL, Chen RZ, Han B, He GC (2009) Identification and characterization of Bph14, a gene conferring resistance to brown planthopper in rice. Proc Natl Acad Sci USA 106:22163–22168
Fan CC, Xing YZ, Mao HL, Lu TT, Han B, Xu CG, Li XH, Zhang QF (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171
Goff SA, Ricke D, Lan TH, Presting G, Wang RL, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong JP, Miguel T, Paszkowski U, Zhang SP, Colbert M, Sun WL, Chen LL, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome Oryza sativa L. ssp. japonica. Science 296:92–100
Gu KY, Yang B, Tian DS, Wu L, Wang DJ, Sreekala C, Yang F, Chu ZQ, Wang GL, White FF, Yin ZC (2005) R gene expression induced by a type-III effector triggers disease resistance in rice. Nature 435:1122–1125
Gu BG, Zhou TY, Luo JH, Liu H, Wang YC, Shangguan YY, Zhu JJ, Li Y, Sang T, Wang ZX, Han B (2015) An-2 encodes a cytokinin synthesis enzyme that regulates awn length and grain production in rice. Mol Plant 8:1635–1650
Hua L, Wang DR, Tan LB, Fu YC, Liu FX, Xiao LT, Zhu ZF, Fu Q, Sun XY, Gu P, Cai HW, McCouch SR, Sun CQ (2015) LABA1, a domestication gene associated with long, barbed awns in wild rice. Plant Cell 27:1875–1888
Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41:494–497
Huang WC, Yu CC, Hu J, Wang LL, Dan ZW, Zhou W, He CL, Zeng YF, Yao GX, Qi JZ, Zhang ZH, Zhu RS, Chen XF, Zhu YG (2015) Pentatricopeptide-repeat family protein RF6 functions with hexokinase 6 to rescue rice cytoplasmic male sterility. Proc Natl Acad Sci 112:14984–14989
Jeung JU, Kim BR, Cho YC, Han SS, Moon HP, Lee YT, Jena KK (2007) A novel gene, Pi40(t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice. Theor Appl Genet 115:1163–1177
Jin J, Hua L, Zhu ZF, Tan LB, Zhao XH, Zhang WF, Liu FX, Fu YC, Cai HW, Sun XY, Gu P, Xie DX, Sun CQ (2016) GAD1 encodes a secreted peptide that regulates grain number, grain length, and awn development in rice domestication. Plant Cell 28:2453–2463
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Li XM, Chao DY, Wu Y, Huang X, Chen K, Cui LG, Su L, Ye WW, Chen H, Chen HC, Dong NQ, Guo T, Shi M, Feng Q, Zhang P, Han B, Shan JX, Gao JP, Lin HX (2015) Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice. Nat Genet 47:827–833
Luo DP, Xu H, Liu ZL, Guo JX, Li HY, Chen LT, Fang C, Zhang QY, Bai M, Yao N, Wu H, Wu H, Ji CH, Zheng HQ, Chen YL, Ye S, Li X, Zhao XC, Li RQ, Liu YG (2013a) A detrimental mitochondrial-nuclear interaction causes cytoplasmic male sterility in rice. Nat Genet 45:573–577
Luo J, Liu H, Zhou T, Gu B, Huang X, Shangguan Y, Zhu J, Li Y, Zhao Y, Wang Y, Zhao Q, Wang A, Wang Z, Sang T, Wang Z, Han B (2013b) An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice. Plant Cell 25:3360–3376
Qi J, Qian Q, Bu QY, Li SY, Chen Q, Sun JQ, Liang WX, Zhou YH, Chu CC, Li XG, Ren FG, Palme K, Zhao BR, Chen JF, Chen MS, Li CY (2008) Mutation of the rice narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol 147:1947–1959
Qiao W, Qi L, Cheng Z, Su L, Li J, Sun Y, Ren J, Zheng X, Yang Q (2016) Development and characterization of chromosome segment substitution lines derived from Oryza rufipogon in the genetic background of O. sativa spp. indica cultivar 9311. BMC Genom 17:580
Qiu YF, Guo JP, Jing SL, Zhu LL, He GC (2012) Development and characterization of japonica rice lines carrying the brown planthopper-resistance genes BPH12 and BPH6. Theor Appl Genet 124:485–494
Qu SH, Liu GF, Zhou B, Bellizzi M, Zeng LR, Dai LY, Han B, Wang GL (2006) The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site–leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172:1901–1914
Reuscher S, Furuta T (2016) ABHgenotypeR: Easy Visualization of ABH Genotypes
SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci 95:1460–1465
Song WY, Wang GL, Chen LL, Kim H, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804–1806
Surzycki S (2000) Preparation of genomic DNA from plant cells. Basic techniques in molecular biology. Springer, Berlin, pp 57–78
Tanabata T, Shibaya T, Hori K, Ebana K, Yano M (2012) SmartGrain: high-throughput phenotyping software for measuring seed shape through image analysis. Plant Physiol 160:1871–1880
Thalapati S, Batchu AK, Neelamraju S, Ramanan R (2012) Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice. Funct Integr Genom 12:277–289
Wang E, Wang J, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH (2008a) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374
Wang ET, Wang JJ, Zhu XD, Hao W, Wang LY, Li Q, Zhang LX, He W, Lu BR, Lin HX, Ma H, Zhang GQ, He ZH (2008b) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374
Wang CL, Zhang XP, Fan YL, Gao Y, Zhu QL, Zheng CK, Qin TF, Li YQ, Che JY, Zhang MW, Yang B, Liu YG, Zhao KJ (2015a) XA23 is an executor R protein and confers broad-spectrum disease resistance in rice. Mol Plant 8:290–302
Wang SK, Li S, Liu Q, Wu K, Zhang JQ, Wang SS, Wang Y, Chen XB, Zhang Y, Gao CX, Wang F, Huang HX, Fu XD (2015b) The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nat Genet 47:949–954
Wang YX, Xiong GS, Hu J, Jiang L, Yu H, Xu J, Fang YX, Zeng LJ, Xu EB, Xu J, Ye WJ, Meng XB, Liu RF, Chen HQ, Jing YH, Wang YH, Zhu XD, Li JY, Qian Q (2015c) Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47:944–948
Wu W, Liu X, Wang M, Meyer RS, Luo X, Ndjiondjop M-N, Tan L, Zhang J, Wu J, Cai H, Sun C, Wang X, Wing RA, Zhu Z (2017) A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nat Plants 3:17064
Xiao JH, Grandillo S, Ahn SN, McCouch SR, Tanksley SD, Li JM, Yuan LP (1996) Genes from wild rice improve yield. Nature 384:223–224
Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708
Xu F, Fang J, Ou S, Gao S, Zhang F, Du L, Xiao Y, Wang H, Sun X, Chu J, Wang G, Chu C (2015) Variations in CYP78A13 coding region influence grain size and yield in rice. Plant Cell Environ 38:800–811
Yang HY, You AQ, Yang ZF, Zhang FT, He RF, Zhu LL, He GC (2004a) High-resolution genetic mapping at the Bph15 locus for brown planthopper resistance in rice (Oryza sativa L.). Theor Appl Genet 110:182–191
Yang YZ, Peng H, Huang HM, Wu JX, Jia SR, Huang DF, Lu TG (2004b) Large-scale production of enhancer trapping lines for rice functional genomics. Plant Sci 167:281–288
Yoshida S, Forno DA, Cock JH, Gomez KA (1971) Laboratory manual for physiological studies of rice, 3rd edn. The International Rice Research Institute, Los BaÑos
Young ND, Tanksley SD (1989) Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theor Appl Genet 77:95–101
Yu J, Hu SN, Wang J, Wong GK-S, Li SG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ, Cao ML, Liu J, Sun JD, Tang JB, Chen YJ, Huang XB, Lin W, Ye C, Tong W, Cong LJ, Geng JN, Han YJ, Li L, Li W, Hu GQ, Huang XG, Li WJ, Li J, Liu ZW, Li L, Liu JP, Qi QH, Liu JS, Li L, Li T, Wang XG, Lu H, Wu TT, Zhu M, Ni PX, Han H, Dong W, Ren XY, Feng XL, Cui P, Li XR, Wang H, Xu X, Zhai WX, Xu Z, Zhang JS, He S, Zhang JG, Xu JC, Zhang KL, Zheng XW, Dong JH, Zeng WY, Tao L, Ye J, Tan J, Ren XD, Chen XW, He J, Liu DF, Tian W, Tian CG, Xia HA, Bao QY, Li G, Gao H, Cao T, Wang J, Zhao WM, Li P, Chen W, Wang XD, Zhang Y, Hu JF, Wang J, Liu S, Yang J, Zhang GY, Xiong YQ, Li ZJ, Mao L, Zhou CS, Zhu Z, Chen RS, Hao BL, Zheng WM, Chen SY, Guo W, Li GJ, Liu SQ, Tao M, Wang J, Zhu LH, Yuan LP, Yang HM (2002) A draft sequence of the rice genome Oryza sativa L. ssp. indica. Science 296:79–92
Zhou Y, Zhu J, Li Z, Yi C, Liu J, Zhang H, Tang S, Gu M, Liang G (2009) Deletion in a quantitative trait gene qpe9-1 associated with panicle erectness improves plant architecture during rice domestication. Genetics 183:315–324
Acknowledgements
Funding was provided by CAAS Innovation Project (Grant No. CAAS-XTCX2016002) and Fundamental Research Funds for central Non-profit scientific Institution (Grant No. 1610392018004)
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by Takuji Sasaki.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Figure S1
The plant stature comparison between LSWR and 9311 (TIFF 3830 kb)
Figure S2
The workflow of IL construction. The workflow of constructing an ideal population of ILs. In the first step, LSWR selected from Lingshui City, China, was treated as “female” and 9311 was treated as “male.” After 7 generations of backcrossing or selfing, the chromosomes from LSWR were introgressed into the 9311 background (TIFF 448 kb)
Figure S3
The physical map based on InDel markers. The markers were named after chromosome No. and physical location. The number before the dash indicates the chromosome No., and the number after the dash multiplied by 100,000 indicates the approximate physical distance (bp). (TIFF 68306 kb)
Figure S4
The Q-PCR analysis for the NAL1 gene expression level. A. Comparison of the NAL1 gene expression level among 9311, No. 28 and No. 63. B. Comparison of the NAL1 gene expression level between Nipponbare (Nip) and Ov1 (TIFF 3002 kb)
Table S1
InDel primers used in this study (XLSX 25 kb)
Table S2
The agricultural trait data of 77 ILs (XLSX 19 kb)
Table S3
The primers related to the Nal1 gene (XLS 19 kb)
Rights and permissions
About this article
Cite this article
Qin, G., Nguyen, H.M., Luu, S.N. et al. Construction of introgression lines of Oryza rufipogon and evaluation of important agronomic traits. Theor Appl Genet 132, 543–553 (2019). https://doi.org/10.1007/s00122-018-3241-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-018-3241-0