Advertisement

High-density genetic map development and QTL mapping for concentration degree of floret flowering date in cultivated peanut (Arachis hypogaea L.)

  • 34 Accesses

Abstract

The concentration degree of floret flowering date (CDFFD) is an important selection index for earliness breeding of peanut, while the genetic basis of CDFFD-related traits in peanut is poorly understood. The aim of this study was to develop a high-density genetic linkage map of cultivated peanut by combining SLAF-seq (specific locus amplified fragment sequencing) with SSR (simple sequence repeat) techniques and to identify QTL (quantitative trait loci) controlling CDFFD. A RIL population derived from a cross between Silihong and Jinonghei 3 was sequenced by the HiSeq 2500 platform. A total of 1262.02 M high-quality paired-end reads were obtained, and 1,328,966 SNPs (single nucleotide polymorphisms) were developed from parents and progenies, of which 754,499 SNPs were successfully encoded and genotyping. The resulting map consisted of 3326 genetic markers (2996 SNPs and 330 SSRs) distributed in 20 linkage groups (LGs), spanning 1822.83 cM with an average distance of 0.55 cM between adjacent markers. These assigned SNP markers had average sequencing depths of 16.94-, 15.66-, and 20.94-fold in the male parent, female parent, and their progenies, respectively. Based on phenotyping in 4 environments, 15 significant QTL for the CDFFD were identified. And one major QTL for days to accumulation of 25 flowers (DA25F), qDA25F6.2, located on chromosome 6 was obtained, with a phenotypic variance explanation (PVE) of 12.49%. This map exhibited higher resolution and accuracy, which will facilitate more QTL discovery for interested agronomic and quality traits in cultivated peanut.

This is a preview of subscription content, log in to check access.

Access options

Buy single article

Instant unlimited access to the full article PDF.

US$ 39.95

Price includes VAT for USA

Subscribe to journal

Immediate online access to all issues from 2019. Subscription will auto renew annually.

US$ 99

This is the net price. Taxes to be calculated in checkout.

Fig. 1
Fig. 2

References

  1. Agarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X, Huang GD, Wang XJ, Deshmukh R, Holbrook CC, Bertioli DJ, Ozias-Akins P, Jackson SA, Varshney RK, Guo BZ (2018) High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnol J 16:1954–1967

  2. Bailey WK, Bear JE (1973) Components of earliness of maturity in peanut (Arachis hypogaea L.). Am Peanut Res Educ Soc 5:32–39

  3. Chen YN, Ren XP, Zheng YL, Zhou XJ, Huang L, Yan LY, Jiao YQ, Chen WG, Huang SM, Wan LY, Lei Y, Liao BS, Huai DX, Wei WH, Jiang HF (2017) Genetic mapping of yield traits using RIL population derived from Fuchuan Dahuasheng and ICG6375 of peanut (Arachis hypogaea L.). Mol Breed 37:17–30

  4. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

  5. Gregory WC, Gregory MP (1976) Groundnut. In: Simmonds NW (ed) Evolution of crop plants. Longman Group Ltd, London, pp 151–154

  6. Gregory WC, Krapovickas A, Gregory MP (1980) Structures, variation, evolution and classification in Arachis. In: Summerfield RJ, Buntiing AH (eds) Advances in legume science. Royal Botanic Gardens, Kew, pp 469–481

  7. Guo GJ, Wang SB, Liu JB, Pan BG, Diao WP, Ge W, Gao CZ, Snyder JC (2017) Rapid identification of QTLs underlying resistance to Cucumber mosaic virus in pepper (Capsicum frutescens). Theor Appl Genet 130:41–52

  8. Hake AA, Shirasawa K, Yadawad A, Sukruth M, Patil M, Nayak SN, Lingaraju S, Patil PV, Nadaf HL, Gowda MVC, Bhat RS (2017) Mapping of important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut (Arachis hypogaea L.). PLoS One 12:e0186113

  9. Halward TM, Stalker HT, Larue EA, Kochert GA (1991) Genetic variation detectable with molecular markers among unadapted germplasm resources of cultivated peanut and related wild species. Genome 34:1013–1020

  10. Halward TM, Stalker HT, Larue EA, Kochert GA (1992) Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). Plant Mol Biol 18:315–325

  11. Halward TM, Stalker HT, Kochert GA (1993) Development of an RFLP linkage map in diploid peanut species. Theor Appl Genet 87:379–384

  12. Herselman L, Thwaites R, Kimmins FM, Courtois B, van der Merwe PJA, Seal SE (2004) Identification and mapping of AFLP markers linked to peanut (Arachis hypogaea L.) resistance to the aphid vector of groundnut rosette disease. Theor Appl Genet 109:1426–1433

  13. Hu XH, Zhang SZ, Miao HR, Cui FG, Shen Y, Yang WQ, Xu TT, Chen N, Chi XY, Zhang ZM, Chen J (2018) High-density genetic map construction and identification of QTLs controlling oleic and linoleic acid in peanut using SLAF-seq and SSRs. Sci Rep 8:5479

  14. Huang XH, Zhao Y, Wei XH, Li CY, Wang AH, Zhao Q, Li WJ, Guo YL, Deng LW, Zhu CR, Fan DL, Lu YQ, Weng QJ, Liu KY, Zhou TY, Jing YF, Si LZ, Dong GJ, Huang T, Lu TT, Feng Q, Qian Q, Li JY, Han B (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–39

  15. Huang L, Ren XP, Wu B, Li XP, Chen WG, Zhou XJ, Chen YN, Pandey MK, Jiao YQ, Luo HY, Lei Y, Varshney RK, Liao BS, Jiang HF (2016) Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.). Sci Rep 6:39478

  16. Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11:38

  17. Ji GS, Zhang QJ, Du RH, Lv P, Ma X, Fan S, Li SY, Hou SL, Han YC, Liu GQ (2017) Construction of a high-density genetic map using specific-locus amplified fragments in sorghum. BMC Genomics 18:51

  18. Khedikar Y, Pandey MK, Sujay V, Singh S, Nayak SN, Klein-Gebbinck HW, Sarvamangala C, Mukri G, Garg V, Upadhyaya HD, Nadaf HL, Gowda MVC, Varshney RK, Bhat RS (2018) Identification of main effect and epistatic quantitative trait loci for morphological and yield-related traits in peanut (Arachis hypogaea L.). Mol Breeding 38:7

  19. Kochert GA, Halward TM, Branch WD, Simpson CE (1991) RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theor Appl Genet 81:565–570

  20. Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugenics 12:172–175

  21. Krapovickas A, Gregory WC (1994) Taxonomia del genero Arachis (Leguminosae). Bonplandia 8:1–186

  22. Li HH, Ribaut JM, Li ZL, Wang JK (2008) Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations. Theor Appl Genet 116:243–260

  23. Li B, Tian L, Zhang JY, Huang L, Han FX, Yan SR, Wang LZ, Zheng HK, Sun JM (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 15:1086

  24. Li B, Fan SX, Yu FK, Chen Y, Zhang SR, Han FX, Yan SR, Wang LZ, Sun JM (2017a) High-resolution mapping of QTL for fatty acid composition in soybean using specific-locus amplified fragment sequencing. Theor Appl Genet 130:1467–1479

  25. Li YJ, Li LZ, Zhang XR, Zhang K, Ma DC, Liu JQ, Wang XJ, Liu FZ, Wan YS (2017b) QTL mapping and marker analysis of main stem height and the first lateral branch length in peanut (Arachis hypogaea L.). Euphytica 213:57–70

  26. Liao BS (2008) Current situation and counter measures of peanut research and industry development in China. China Agric Inf 18–20:22 (in Chinese)

  27. Liu DY, Ma CX, Hong WG, Huang L, Liu M, Liu H, Zeng HP, Deng DJ, Xin HG, Song J, Xu CH, Sun XW, Hou XL, Wang XW, Zheng HK (2014) Construction and analysis of high-density linkage map using high-throughput sequencing data. PLoS One 9:e98855

  28. Luo X, Chen T, Zeng XL, He DW, He YH (2019) Feedback regulation of FLC by FLOWERING LOCUS T (FT) and FD through a 5’ FLC promoter region in Arabidopsis. Mol Plant 12:285–288

  29. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a map reduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

  30. Meng L, Li HH, Zhang LY, Wang JK (2015) QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J 3:169–173

  31. Paik-Ro OG, Smith RL, Knauft DA (1992) Restriction fragment length polymorphism evaluation of six peanut species within the Arachis section. Theor Appl Genet 84:201–208

  32. Pei RL, Zhang JY, Tian L, Zhang SR, Han FX, Yan SR, Wang LZ, Li B, Sun JM (2018) Identification of novel QTL associated with soybean isoflavone content. Crop J 6:244–252

  33. Qin ZR, Bai YX, Muhammad S, Wu X, Deng PC, Wu JJ, An HL, Wu L (2019) Divergent roles of FT-like 9 in flowering transition under different day lengths in Brachypodium distachyon. Nat Commun 10:812

  34. Ravi K, Vadez V, Isobe S, Mir RR, Guo Y, Nigam SN, Gowda MVC, Radhakrishnan T, Bertioli DJ, Knapp SJ, Varshney RK (2011) Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.). Theor Appl Genet 122:1119–1132

  35. Shilman F, Brand Y, Brand A, Hedvat I, Hovav R (2011) Identification and molecular characterization of homeologous Δ9-stearoyl acyl carrier protein desaturase 3 genes from the allotetraploid peanut (Arachis hypogaea L.). Plant Mol Biol Rep 29:232–241

  36. Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C, Naito Y, Kuboyama T, Nakaya A, Sasamoto S, Watanabe A, Kato M, Kawashima K, Kishida Y, Kohara M, Kurabayashi A, Takahashi C, Tsuruoka H, Wada T, Isobe S (2012) In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol 12:80

  37. Sun DR (1998) Peanut breeding. China Agriculture Press, Beijing, China (in Chinese)

  38. Sun XW, Liu DY, Zhang XF, Li WB, Liu H, Hong WG, Jiang CB, Guan N, Ma CX, Zeng HP, Xu CH, Song J, Huang L, Wang CM, Shi JJ, Wang R, Zheng XH, Lu CY, Wang XW, Zheng HK (2013) SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One 8:e58700

  39. Tian YK, Zheng H, Zhang F, Wang SL, Ji XR, Xu C, He YH, Ding Y (2019) PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR. Sci Adv 5:eaau7246

  40. Upadhyaya HD, Nigam SN (1994) Inheritance of two components of early maturity in groundnut (Arachis hypogaea L.). Euphytica 78:59–67

  41. Upadhyaya HD, Swamy BPM, Goudar PVK, Kullaiswamy BY, Singh S (2005) Identification of diverse groundnut germplasm through multi-environment evaluation of a core collection for Asia. Field Crop Res 93:293–299

  42. van Os H, Stam P, Visser RG, van Eck HJ (2005) SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data. Theor Appl Genet 112:187–194

  43. Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247–252

  44. Varshney RK, Bertioli DJ, Moretzsohn MC, Vadez V, Krishnamurthy L, Aruna R, Nigam SN, Moss BJ, Seetha K, Ravi K, He G, Knapp SJ, Hoisington DA (2009) The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theor Appl Genet 118:729–739

  45. Wang CT, Zhang JC (2013) Genetic improvement of peanut. Shanghai science and technology press, Shanghai (in Chinese)

  46. Wang H, Penmetsa RV, Yuan M, Gong LM, Zhao YL, Guo BZ, Farmer AD, Rosen BD, Gao JL, Isobe S, Bertioli DJ, Varshney RK, Cook DR, He GH (2012) Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.). BMC Plant Biol 12:10

  47. Wang MQ, Xu YH, Wu ZD, Wang HZ, Zhang HG (2017) High-density genetic map construction in sugar beet (Beta vulgaris L.) by high-throughput technology. Sugar Tech 20:212–219

  48. Wang ZH, Huai DX, Zhang ZH, Cheng K, Kang YP, Wan LY, Yan LY, Jiang HF, Lei Y, Liao BS (2018) Development of a high-density genetic map based on specific length amplified fragment sequencing and its application in quantitative trait loci analysis for yield-related traits in cultivated peanut. Front Plant Sci 9:827

  49. Wang L, Yang XL, Cui SL, Mu GJ, Sun XM, Liu LF, Li ZC (2019a) QTL mapping and QTL×environment interaction analysis of multi-seed pod in cultivated peanut (Arachis hypogaea L.). Crop J 7:249–260

  50. Wang YH, Tan JY, Wu ZM, VandenLangenberg K, Wehner TC, Wen CL, Zheng XY, Owens K, Thornton A, Bang HH, Hoeft E, Kraan PAG, Suelmann J, Pan JS, Weng YQ (2019b) STAYGREEN, STAY HEALTHY: a loss-of-susceptibility mutation in the STAYGREEN gene provides durable, broad-spectrum disease resistances for over 50 years of US cucumber production. New Phytol 221:415–430

  51. West MA, van Leeuwen H, Kozik A, Kliebenstein DJ, Doerge RW, St Clair DA, Michelmore RW (2006) High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Res 16:787–795

  52. Wu YH, Bhat PR, Close TJ, Lonardi S (2008) Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet 4:e1000212

  53. Yi LX, Gao FY, Siqin B, Zhou Y, Li Q, Zhao XQ, Jia XY, Zhang H (2017) Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology. PLoS One 12:e0189785

  54. Yu SL (2011) Chinese peanut genetics and breeding. Shanghai science and technology press, Shanghai, pp 208–218 (in Chinese)

  55. Yu HF, Wang JS, Zhao ZQ, Sheng XG, Shen YS, Branca F, Gu HH (2019) Construction of a high-density genetic map and identification of loci related to hollow stem trait in broccoli (Brassica oleracea L. italica). Front Plant Sci 10:45

  56. Zhang YX, Wang LH, Xin HG, Li DH, Ma CX, Ding X, Hong WG, Zhang XR (2013) Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Plant Biol 13:141

  57. Zhang Z, Ge Q, Liu AY, Li JW, Gong JW, Shang HH, Shi YZ, Chen TT, Wang YL, Palanga KK, Muhammad J, Lu QW, Deng XY, Tan YN, Liu RX, Zou XY, Rashid H, Iqbal MS, Gong WK, Yuan YL (2017) Construction of a high-density genetic map and its application to QTL identification for fiber strength in upland cotton. Crop Sci 57:774–788

  58. Zhang YW, Li W, Lin YH, Zhang LF, Wang CJ, Xu R (2018) Construction of a high-density genetic map and mapping of QTLs for soybean (Glycine max) agronomic and seed quality traits by specific length amplified fragment sequencing. BMC Genomics 19:641

  59. Zhou XJ, Xia YL, Ren XP, Chen YN, Huang L, Huang SM, Liao BS, Lei Y, Yan LY, Jiang HF (2014) Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRAD-seq). BMC Genomics 15:351

  60. Zhu ZZ, Li XQ, Wei Y, Guo SB, Sha AH (2018) Identification of a novel QTL for panicle length from wild rice (Oryza minuta) by specific locus amplified fragment sequencing and high density genetic mapping. Front Plant Sci 9:1492

  61. Zicola J, Liu LY, Tanzler P, Turck F (2019) Targeted DNA methylation represses two enhancers of FLOWERING LOCUS T in Arabidopsis thaliana. Nat Plants 5:300–307

Download references

Acknowledgments

We thank Zhanying Zhang, Xingming Sun, Jianyin Xie, Haifeng Guo, and Dongdong Li (College of Agronomy, China Agricultural University, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education) for providing important advice during manuscript preparation. And we also thank Zhenzhen Wang and Jian Li (Beijing Biomarker Technologies Corporation, China) for providing sequencing technical support.

Funding information

This work was supported by the China Agriculture Research System (CARS-13), the National Natural Science Foundation of China (31771833), the Science and Technology Supporting Plan Project of Hebei Province, China (16226301D), and the Key Projects of Science and Technology Research in Higher Education Institution of Hebei Province, China (ZD2015056).

Author information

L.L. (Lifeng Liu) and Z.L. conceived the original research plans. X.Y. and S.C. designed the experiments. N.Z. and L.L. (Li Li) performed part of the experiments. L.W., M.H., and G.M. analyzed the data. L.W. wrote the manuscript. All authors listed have revised and approved the manuscript.

Correspondence to Lifeng Liu or Zichao Li.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

This article does not contain any studies with human participants or animals performed by the any authors.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

ESM 1

(DOC 7968 kb)

ESM 2

(DOC 21 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Wang, L., Yang, X., Cui, S. et al. High-density genetic map development and QTL mapping for concentration degree of floret flowering date in cultivated peanut (Arachis hypogaea L.). Mol Breeding 40, 17 (2020). https://doi.org/10.1007/s11032-019-1083-3

Download citation

Keywords

  • Genetic map
  • SLAF-seq
  • SNP
  • SSR
  • Concentration degree of floret flowering date (CDFFD)
  • QTL mapping