Advertisement

Molecular Breeding

, 39:106 | Cite as

Construction of the first high-density genetic map and QTL mapping for photosynthetic traits in Lycium barbarum L.

  • Haiguang Gong
  • Fazal Rehman
  • Tianshun Yang
  • Zhong Li
  • Shaohua Zeng
  • Lizhu Pan
  • Yongqing Li
  • Ying WangEmail author
Article
  • 41 Downloads

Abstract

Photosynthesis is essential for plant development as well as crop yield. QTL mapping was conducted for photosynthetic traits such as net photosynthetic rate (PN), stomatal conductance (Cond), inner-cellular carbon dioxide (Ci), transpiration rate (Trmmol), limiting value of the stoma (Ls), and water use efficiency (WUE). A high-density genetic map covering 964.03 cM was developed based on a hybrid population of the Goji (Lycium barbarum L.). The genetic map consisted of 23,967 markers with an average distance of 0.040 cM between two adjacent markers. Twenty-nine and three quantitative trait loci (QTLs) for photosynthetic traits and trunk diameter (TD), respectively, were detected, of which 8 QTLs, including 3 for PN, 2 for Cond, 1 for Trmmol, 1 for Ci, and 1 for Ls, can be detected in at least 2-year measurements (from 2017 and 2018, as well as the averaged data from 2017 and 2018, which was regarded as a 3rd year, named 1718). Among these measurements, qPN1 was detected in all 3 years and considered a stable QTL whereas qLs1 and qLs2 with the highest phenotypic variance explained (PVE%) 32.012 and 17.965 were detected as major QTLs. PN, Cond, Ci, Trmmol, Ls, and WUE showed significant correlations with each other except for Cond and WUE whereas PN and Cond were significantly correlated with TD (P < 0.05). These findings indicate that PN and Cond are critical factors for the growth of plants and QTLs contribute to PN, Cond, and TD, which could provide an improved way to enhance the breeding of the Goji in relation to its growth rate.

Keywords

Genetic map ddRAD-seq QTL mapping Goji berry Photosynthesis 

Notes

Acknowledgments

We also would like to thank Professor Kede Liu for his kind suggestions and help with the data analysis. We appreciated Bairuiyuan Company and Northwest Agriculture Research Center for their help with maintaining the goji orchard.

Funding information

This work was supported by the National Key R&D Project of China (2018YFD1000607), a grant from the Chinese Academy of Sciences (XDA13020604), National Natural Science Foundation of China (31770334), Youth Innovation Promotion Association CAS (2015286), and Ningxia Agricultural Comprehensive Development Science and Technology Project (NTKJ2018-07).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11032_2019_1000_MOESM1_ESM.docx (1.6 mb)
ESM 1 (DOCX 1646 kb)
11032_2019_1000_MOESM2_ESM.pdf (131 kb)
ESM 2 (PDF 131 kb)
11032_2019_1000_MOESM3_ESM.emf (1.3 mb)
ESM 3 (EMF 1348 kb)
11032_2019_1000_MOESM4_ESM.xlsx (33 kb)
ESM 4 (XLSX 32 kb)
11032_2019_1000_MOESM5_ESM.xlsx (859 kb)
ESM 5 (XLSX 858 kb)
11032_2019_1000_MOESM6_ESM.xlsx (12 kb)
ESM 6 (XLSX 12 kb)

References

  1. Akond M, Liu S, Schoener L, Anderson JA, Kantartzi SK, Meksem K, Song Q, Wang D, Wen Z, Lightfoot DA, Kassem MA (2013) A SNP-based genetic linkage map of soybean using the SoyS - NP6K Illumina Infinium BeadChip genotyping Array. Plant Genetics, Genomics, and Biotechnology 1:80–89CrossRefGoogle Scholar
  2. Amagase H, Farnsworth NR (2011) A review of botanical characteristics, phytochemistry, clinical relevance in efficacy and safety of Lycium barbarum fruit (Goji). Food Res Int 44:1702–1717CrossRefGoogle Scholar
  3. Barria A, Christensen KA, Yoshida GM, Correa K, Jedlicki A, Lhorente JP, Davidson WS, Yanez JM (2018) Genomic predictions and genome-wide association study of resistance against Piscirickettsia salmonis in Coho Salmon (Oncorhynchus kisutch) using ddRAD sequencing. G3-Genes Genomes Genetics 8:1183–1194PubMedCentralGoogle Scholar
  4. Baxter SW, Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD, Blaxter ML (2011) Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS One 6:e19315CrossRefGoogle Scholar
  5. Brauer CJ, Unmack PJ, Beheregaray LB (2017) Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish. Mol Ecol 26:6841–6856CrossRefGoogle Scholar
  6. Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3-Genes Genomes Genetics 1:171–182PubMedCentralGoogle Scholar
  7. Chang RCC, Ho YS, So KF (2015) Wolfberry as anti-aging to prevent and delay neurodegeneration in Alzheimer’s disease. In: International conference on food factors. ICoFF2015Google Scholar
  8. Che Y, Song N, Yang Y, Yang X, Duan Q, Zhang Y, Lu Y, Li X, Zhang J, Li X, Zhou S, Li L, Liu W (2018) QTL mapping of six spike and stem traits in hybrid population of Agropyron Gaertn in multiple environments. Front Plant Sci 9Google Scholar
  9. Chen YP, Chen YN, Li WH, Xu CC (2006) Characterization of photosynthesis of Populus euphratica grown in the arid region. Photosynthetica 44:622–626CrossRefGoogle Scholar
  10. Chen J, Liu X, Zhu L, Wang Y (2013) Nuclear genome size estimation and karyotype analysis of Lycium species (Solanaceae). Sci Hortic 151:46–50CrossRefGoogle Scholar
  11. Chen Z, Wang B, Dong X, Liu H, Ren L, Chen J, Hauck A, Song W, Lai J (2014) An ultra-high-density bin-map for rapid QTL mapping for tassel and ear architecture in a large F-2 maize population. BMC Genomics 15:433CrossRefGoogle Scholar
  12. Chen J, Wang N, Fang L, Liang Z, Li S, Wu B (2015) Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries. BMC Plant Biol 15:28CrossRefGoogle Scholar
  13. Chen WJ, Sun XF, Zhang RX, Xu MJ, Dou TH, Zhang XB, Zhong M, Yang WQ, Liu L, Lu XY, Zhu CQ (2017a) Hypertriglyceridemic acute pancreatitis in the emergency department: typical clinical features and genetic variants. J Dig Dis 18:359–368CrossRefGoogle Scholar
  14. Chen C, Xu M, Wang C, Qiao G, Wang W, Tan Z, Wu T, Zhang Z (2017b) Characterization of the Lycium barbarum fruit transcriptome and development of EST-SSR markers. PLoS One 12Google Scholar
  15. Chen J, Chao CT, Wei X (2018) Gojiberry breeding: current status and future prospects. InBreeding and health benefits of fruit and nut crops 10. IntechOpenGoogle Scholar
  16. DaCosta JM, Sorenson MD (2016) ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: analyses of two avian genera with contrasting histories. Mol Phylogenet Evol 94:122–135CrossRefGoogle Scholar
  17. Dahech I, Farah W, Trigui M, Ben Hssouna A, Belghith H, Belghith KS, Ben Abdallah F (2013) Antioxidant and antimicrobial activities of Lycium shawii fruits extract. Int J Biol Macromol 60:328–333CrossRefGoogle Scholar
  18. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510CrossRefGoogle Scholar
  19. Davik J, Sargent DJ, Brurberg MB, Lien S, Kent M, Alsheikh M (2015) A ddRAD based linkage map of the cultivated strawberry, Fragaria xananassa. PLoS One 10:e0137746CrossRefGoogle Scholar
  20. Fu B, Liu H, Yu X, Tong J (2016) A high-density genetic map and growth-related QTL mapping in bighead carp (Hypophthalmichthys nobilis). Sci Rep 6Google Scholar
  21. Gong D, Huang L, Xu X, Wang C, Ren M, Wang C, Chen M (2016) Construction of a high-density SNP genetic map in fluecured tobacco based on SLAF-seq. Mol Breed 36Google Scholar
  22. Han K, Lee HY, Ro NY, Hur OS, Lee JH, Kwon JK, Kang BC (2018) QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum. Plant Biotechnol J 16(9):1546–1558CrossRefGoogle Scholar
  23. Harrington G (1979) Estimation of above-ground biomass of trees and shrubs in a Eucalyptus-Populnea F Muell woodland by regression of mass on trunk diameter and plant height. Aust J Bot 27:135–143CrossRefGoogle Scholar
  24. Herve D, Fabre F, Berrios EF, Leroux N, Al Chaarani G, Planchon C, Sarrafi A, Gentzbittel L (2001) QTL analysis of photosynthesis and water status traits in sunflower (Helianthus annuus L.) under greenhouse conditions. J Exp Bot 52:1857–1864CrossRefGoogle Scholar
  25. Hund A, Ruta N, Liedgens M (2009) Rooting depth and water use efficiency of tropical maize inbred lines, differing in drought tolerance. Plant Soil 318:311–325CrossRefGoogle Scholar
  26. Kai W, Nomura K, Fujiwara A, Nakamura Y, Yasuike M, Ojima N, Masaoka T, Ozaki A, Kazeto Y, Gen K, Nagao J, Tanaka H, Kobayashi T, Ototake M (2014) A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication. BMC Genomics 15:233CrossRefGoogle Scholar
  27. Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N (2013) A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae). BMC Genomics 14:32CrossRefGoogle Scholar
  28. Laila R, Park J, Robin AHK, Natarajan S, Vijayakumar H, Shirasawa K, Isobe S, Kim H, Nou I (2019) Mapping of a novel clubroot resistance QTL using ddRAD-seq in Chinese cabbage (Brassica rapa L.). BMC Plant Biol 19:13CrossRefGoogle Scholar
  29. Li S, Wang C, Chang X, Jing R (2012) Genetic dissection of developmental behavior of grain weight in wheat under diverse temperature and water regimes. Genetica 140:393–405CrossRefGoogle Scholar
  30. Li Y, Fan Y, Dai G, Qin K, Cao Y (2013) Cloning of Lycium barbarum Callase gene and expression analysis in male sterile material. Xibei Zhiwu Xuebao 33:437–443Google Scholar
  31. Li B, Tian L, Zhang J, Huang L, Han F, Yan S, Wang L, Zheng H, Sun J (2014) Construction of a high density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max. BMC Genomics 15:1086CrossRefGoogle Scholar
  32. Li N, Yin Y, Wang F, Yao M (2018) Construction of a high-density genetic map and identification of QTLs for cucumber mosaic virus resistance in pepper (Capsicum annuum L.) using specific length amplified fragment sequencing (SLAF-seq). Breed Sci 68:233–241CrossRefGoogle Scholar
  33. Liu GF, Yang J, Xu HM, Hayat Y, Zhu J (2008) Genetic analysis of grain yield conditioned on its component traits in rice (Oryza sativa L.). Aust J Agric Res 59:189–195CrossRefGoogle Scholar
  34. Liu Z, Zhu H, Liu Y, Kuang J, Zhou K, Liang F, Liu Z, Wang D, Ke W (2016) Construction of a high-density, high-quality genetic map of cultivated lotus (Nelumbo nucifera) using next-generation sequencing. BMC Genomics 17Google Scholar
  35. Long SP, Marshall-Colon A, Zhu X (2015) Meeting the global food demand of the future by engineering crop photosynthesis and yield potential. Cell 161:56–66CrossRefGoogle Scholar
  36. Migicovsky Z, Myles S (2017) Exploiting wild relatives for genomics-assisted breeding of perennial crops. Front Plant Sci 4(8):460Google Scholar
  37. Mullet JE, Whitsitt MS (1996) Plant cellular responses to water deficit. Plant Growth Regul 20:119–124CrossRefGoogle Scholar
  38. Murray MG, Thompson WF (1980) Rapid isolation of high molecular-weight plant DNA. Nucleic Acids Res 8:4321–4325CrossRefGoogle Scholar
  39. Niklas KI (1995) Size-dependent allometry of tree height, diameter and trunk-taper. Ann Bot 75:217–227CrossRefGoogle Scholar
  40. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135CrossRefGoogle Scholar
  41. Phadnis N, Orr HA (2009) A single gene causes both male sterility and segregation distortion in Drosophila hybrids. Science 323:376–379CrossRefGoogle Scholar
  42. Pinheiro HA, DaMatta FM, Chaves A, Fontes E, Loureiro ME (2004) Drought tolerance in relation to protection against oxidative stress in clones of Coffea canephora subjected to long-term drought. Plant Sci 167:1307–1314CrossRefGoogle Scholar
  43. Qiu S, Chen J, Chen X, Fan Q, Zhang C, Wang D, Li X, Chen X, Chen X, Liu C, Gao Z, Li H, Hu Y (2014) Optimization of selenylation conditions for Lycium barbarum polysaccharide based on antioxidant activity. Carbohydr Polym 103:148–153CrossRefGoogle Scholar
  44. Qu M, Zheng G, Hamdani S, Essemine J, Song Q, Wang H, Chu C, Sirault X, Zhu X (2017) Leaf photosynthetic parameters related to biomass accumulation in a global rice diversity survey. Plant Physiol 175:248–258CrossRefGoogle Scholar
  45. Rastas P (2017) Lep-MAP 3: robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics 33:3726–3732CrossRefGoogle Scholar
  46. Richards RA (2000) Selectable traits to increase crop photosynthesis and yield of grain crops. J Exp Bot 51:447–458CrossRefGoogle Scholar
  47. Roche D (2015) Stomatal conductance is essential for higher yield potential of C-3 crops. Crit Rev Plant Sci 34:429–453CrossRefGoogle Scholar
  48. Rochette NC, Catchen JM (2017) Deriving genotypes from RAD-seq short-read data using stacks. Nat Protoc 12(12):2640–2659CrossRefGoogle Scholar
  49. Sanchez-Perez R, Dicenta F, Martinez-Gomez P (2012) Inheritance of chilling and heat requirements for flowering in almond and QTL analysis. Tree Genet Genomes 8:379–389CrossRefGoogle Scholar
  50. Schupbach T, Wieschaus E (1991) Female sterile mutations on the 2nd chromosome of Drosophila melanogaster. 2. Mutations blocking oogenesis or altering egg morphology. Genetics 129:1119–1136PubMedPubMedCentralGoogle Scholar
  51. Sinclair TR (2017) Water-conservation traits to increase crop yields in water-deficit environments case studies introduction. In: Springerbriefs in Environmental Science. Sinclair TR (ed). pp 1–3Google Scholar
  52. Singh BD, Singh AK (2015) Marker-assisted plant breeding: principles and practices [M]. Springer, New DelhiCrossRefGoogle Scholar
  53. Solberg TR, Sonesson AK, Woolliams JA, Meuwissen THE (2008) Genomic selection using different marker types and densities. J Anim Sci 86:2447–2454CrossRefGoogle Scholar
  54. Stadler LJ (1931) The experimental modification of heredity in crop plants: I. induced chromosomal irregularities. Sci Agric 11:557–572Google Scholar
  55. State Forestry Administration of China (SFAC) (2018) China Forestry Statistics yearbook-2017. China Forestry Publishing, BeijingGoogle Scholar
  56. Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H, Xu C, Song J, Huang L, Wang C, Shi J, Wang R, Zheng X, Lu C, Wang X, Zheng H (2013) SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One 8Google Scholar
  57. Wang CC, Chang SC, Inbaraj BS, Chen BH (2010a) Isolation of carotenoids, flavonoids and polysaccharides from Lycium barbarum L. and evaluation of the antioxidant activity. Food Chem 120:184–192CrossRefGoogle Scholar
  58. Wang J, Hu Y, Wang D, Zhang F, Zhao X, Abula S, Fan Y, Guo L (2010b) Lycium barbarum polysaccharide inhibits the infectivity of Newcastle disease virus to chicken embryo fibroblast. Int J Biol Macromol 46:212–216CrossRefGoogle Scholar
  59. Wang N, Fang L, Xin H, Wang L, Li S (2012) Construction of a high-density genetic map for grape using next-generation restriction-site associated DNA sequencing. BMC Plant Biol 12:148CrossRefGoogle Scholar
  60. Wang S, Suh JH, Zheng X, Wang Y, Ho C (2017) Identification and quantification of potential anti-inflammatory hydroxycinnamic acid amides from wolfberry. J Agric Food Chem 65:364–372CrossRefGoogle Scholar
  61. Wang L, Zhou X, Ren X, Huang L, Luo H, Chen Y, Chen W, Liu N, Liao B, Lei Y, Yan L, Shen J, Jiang H (2018) A major and stable QTL for bacteria wilt resistance on chromosome B02 identified using a high-density SNP-based genetic linkage map in cultivated Peanut Yuanza 9102 derived population. Front Genet 9Google Scholar
  62. Wu Z, Wang B, Chen X, Wu J, King GJ, Xiao Y, Liu K (2016) Evaluation of linkage disequilibrium pattern and association study on seed oil content in Brassica napus using ddRAD sequencing. PLoS One 11Google Scholar
  63. Xu YB (2010) Molecular Plant Breeding. Oxfordshire, CABI PublishingGoogle Scholar
  64. Xu X, Xu R, Zhu B, Yu T, Qu W, Lu L, Xu Q, Qi X, Chen X (2015) A high-density genetic map of cucumber derived from specific length amplified fragment sequencing (SLAF-seq). Front Plant Sci 5Google Scholar
  65. Xu Y, Li S, Li L, Ma F, Fu X, Shi Z, Xu H, Ma P, An D (2017) QTL mapping for yield and photosynthetic related traits under different water regimes in wheat. Mol Breed 37Google Scholar
  66. Yao R, Heinrich M, Zou Y, Reich E, Zhang X, Chen Y, Weckerle CS (2018) Quality variation of goji (fruits of Lycium spp.) in China: a comparative morphological and Metabolomic analysis. Front Pharmacol 9Google Scholar
  67. Yin G, Dang Y (2008) Optimization of extraction technology of the Lycium barbarum polysaccharides by Box-Behnken statistical design. Carbohydr Polym 74:603–610CrossRefGoogle Scholar
  68. Zelitch I (1982) The close relationship between net photosynthesis and crop yield. Bioscience 32:796–802CrossRefGoogle Scholar
  69. Zhang L, Meng L, Wu W, Wang J (2015) GACD: integrated software for genetic analysis in clonal F-1 and double cross populations. J Hered 106:741–744PubMedGoogle Scholar
  70. Zhang J, Long Y, Wang L, Dang Z, Zhang T, Song X, Dang Z, Pei X (2018) Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.). BMC Plant Biol 18Google Scholar
  71. Zhao X, Xu J, Zhao M, Lafitte R, Zhu L, Fu B, Gao Y, Li Z (2008) QTLs affecting morph-physiological traits related to drought tolerance detected in overlapping introgression lines of rice (Oryza sativa L.). Plant Sci 174:618–625CrossRefGoogle Scholar
  72. Zhao W, Chung J, Cho Y, Rha W, Lee G, Ma K, Han S, Bang K, Park C, Kim S, Park Y (2010) Molecular genetic diversity and population structure in Lycium accessions using SSR markers. Comptes Rendus Biologies 333:793–800CrossRefGoogle Scholar
  73. Zhao Q, Dong B, Chen J, Zhao B, Wang X, Wang L, Zha S, Wang Y, Zhang J, Wang Y (2015) Effect of drying methods on physicochemical properties and antioxidant activities of wolfberry (Lycium barbarum) polysaccharide. Carbohydr Polym 127:176–181CrossRefGoogle Scholar
  74. Zhou X, Xia Y, Ren X, Chen Y, Huang L, Huang S, Liao B, Lei Y, Yan L, Jiang H (2014) Construction of an SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genomics 15:351CrossRefGoogle Scholar
  75. Zhu Y, Yin Y, Yang K, Li J, Sang Y, Huang L, Fan S (2015) Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L) BMC Genomics 16(1):614Google Scholar
  76. Zhu J, Guo Y, Su K, Liu Z, Ren Z, Li K, Guo X (2018) Construction of a highly saturated genetic map for Vitis by next-generation restriction site-associated DNA sequencing. BMC Plant Biol 18(1):347CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Haiguang Gong
    • 1
    • 2
  • Fazal Rehman
    • 1
    • 2
  • Tianshun Yang
    • 1
  • Zhong Li
    • 3
  • Shaohua Zeng
    • 1
    • 4
  • Lizhu Pan
    • 1
  • Yongqing Li
    • 1
    • 2
  • Ying Wang
    • 1
    • 2
    Email author
  1. 1.Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouPeople’s Republic of China
  2. 2.University of Chinese Academy of SciencesBeijingPeople’s Republic of China
  3. 3.Bairuiyuan CompanyYinchuanPeople’s Republic of China
  4. 4.GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, Gannan Normal UniversityGanzhouPeople’s Republic of China

Personalised recommendations