Plant Breeding and Biotechnology

The Korean Society of Breeding Science (한국육종학회)
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Mapping of Quantitative Trait Loci for Yield and Grade Related Traits in Peanut (Arachis hypogaea L.) Using High-Resolution SNP Markers

  • Liang, Yuya (Department of Soil and Crop Sciences, Texas A&M University, College Station) ;
  • Baring, Michael R. (Department of Soil and Crop Sciences, Texas A&M University, College Station) ;
  • Septiningsih, Endang M. (Department of Soil and Crop Sciences, Texas A&M University, College Station)
  • Received : 2018.10.19
  • Accepted : 2018.11.19
  • Published : 2018.12.01
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Abstract

Yield and grade are the key factors that affect production value of peanut. The objective of this study was to identify QTLs for pod yield, hundred-seed weight, and total sound mature kernel (TSMK). A total of 90 recombinant inbred lines, derived from Tamrun OL07 and a breeding line Tx964117, were used as a mapping population and planted in Brownfield and Stephenville, Texas. A genetic map was developed using 1,211 SNP markers based on double digest restriction-site associated DNA sequencing (ddRAD-seq). A total of 10 QTLs were identified above the permutation threshold, three for yield, three for hundred-seed weight and four for TSMK, with LOD score values of 3.7 - 6.9 and phenotypic variance explained of 12.2% - 35.9%. Among those, there were several QTLs that were detected in more than one field experiment. The commonly detected QTLs in this study may be used as potential targets for future breeding program to incorporate yield and grade related traits through molecular breeding.

Keywords

Acknowledgement

Supported by : National Institute of Food and Agriculture

References

  1. Arnold JA III, Beasley JP Jr., Harris GH, Grey TL, Cabrera M. 2017. Effect of gypsum application rate, soil type, and soil calcium on yield, grade and seed quality of runner type peanut cultivars. Peanut Science 44: 13-18. https://doi.org/10.3146/PS16-16.1
  2. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, et al. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3: e3376. https://doi.org/10.1371/journal.pone.0003376
  3. Baring MR, Simpson CE, Burow MD, Black MC, Cason JM, Ayers J, et al. 2006. Registration of 'Tamrun OL07' peanut. Crop Sci. 46: 2721-2722. https://doi.org/10.2135/cropsci2006.06.0413
  4. Brown JKM. 2002. Yield penalties of disease resistance in crops. Curr. Opin. Plant Biol. 5: 339-344. https://doi.org/10.1016/S1369-5266(02)00270-4
  5. Buerstmayr H, Ban T, Anderson JA. 2009. QTL mapping and marker-assisted selection for Fusarium head blight resistance in wheat: a review. Plant Breed. 128: 1-26. https://doi.org/10.1111/j.1439-0523.2008.01550.x
  6. Burow MD, Starr JL, Park C-H, Simpson CE, Paterson AH. 2014. Introgression of homeologous quantitative trait loci (QTLs) for resistance to the root-knot nematode [Meloidogyne arenaria (Neal) chitwood] in an advanced backcross-QTL population of peanut (Arachis hypogaea L.). Mol. Breed. 34: 393-406. https://doi.org/10.1007/s11032-014-0042-2
  7. Faircloth WH, Prostko EP. 2010. Effect of imazapic and 2,4-DB on peanut yield, grade, and seed germination. Peanut Science 37: 78-82. https://doi.org/10.3146/PS09-011.1
  8. Gautami B, Fonceka D, Pandey MK, Moretzsohn MC, Sujay V, Qin H, et al. 2012. An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS One 7: e41213. https://doi.org/10.1371/journal.pone.0041213
  9. Gomez Selvaraj M, Narayana M, Schubert AM, Ayers JL, Baring MR, Burow MD. 2009. Identification of QTLs for pod and kernel traits in cultivated peanut by bulked segregant analysis. Electron. J. Biotechnol. 12: 1-10. doi:10.2225/vol12-issue2-fulltext-13.
  10. He G, Meng R, Gao H, Guo B, Gao G, Newman M, et al. 2005. Simple sequence repeat markers for botanical varieties of cultivated peanut (Arachis hypogaea L.). Euphytica 142: 131-136. https://doi.org/10.1007/s10681-005-1043-3
  11. Khedikar YP, Gowda MVC, Sarvamangala C, Patgar KV, Upadhyaya HD, Varshney RK. 2010. A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.). Theor. Appl. Genet. 121: 971-984. https://doi.org/10.1007/s00122-010-1366-x
  12. Lander E, Kruglyak L. 1995. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat. Genet. 11: 241-247. https://doi.org/10.1038/ng1195-241
  13. Liang X, Zhou G, Hong Y, Chen X, Liu H, Li S. 2009. Overview of research progress on peanut (Arachis hypogaea L.) host resistance to aflatoxin contamination and genomics at the guangdong academy of agricultural sciences. Peanut Science 36: 29-34. https://doi.org/10.3146/AT07-003.1
  14. Liang Y, Baring M, Wang S, Septiningsih EM. 2017. Mapping QTLs for leafspot resistance in peanut using snp-based next-generation sequencing markers. Plant Breed. Biotech. 5: 115-122. https://doi.org/10.9787/PBB.2017.5.2.115
  15. Mallikarjuna N, Varshney RK. 2014. Genetics, genomics and breeding of peanuts. CRC Press, Boca Raton, Florida.
  16. McCough SR, Doerge RW. 1995. QTL mapping in rice.Trends Genet. 11: 482-487.
  17. Moretzsohn M, Hopkins M, Mitchell S, Kresovich S, Valls J, Ferreira M. 2004. Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol. 4: 11. https://doi.org/10.1186/1471-2229-4-11
  18. 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: e37135. https://doi.org/10.1371/journal.pone.0037135
  19. Porter DM, Melouk HA. 1997. Sclerotinia blight, p. 34-35. In: N. Kokalis-Burelle, DM. Porter, R. Rodriguez-Kabana, DH. Smith, P. Subrahmanyam (eds.). Compendium of peanut diseases. 2nd ed. APS PRESS, St. Paul, Minnesota.
  20. Ravi K, Vadez V, Isobe S, Mir RR, Guo Y, Nigam SN, et al. 2010. 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.
  21. Sharp GL, Martin JM, Lanning SP, Blake NK, Brey CW, Sivamani E, et al. 2002. Field evaluation of transgenic and classical sources of wheat streak mosaic virus resistance. Crop Sci. 42: 105-110.
  22. Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, et al. 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. https://doi.org/10.1186/1471-2229-12-80
  23. Simpson CE, Baring MR, Schubert AM, Melouk HA, Black MC, Lopez Y, et al. 2003. Registration of 'Tamrun OL01' peanut. Crop Sci. 43: 2298-2299. https://doi.org/10.2135/cropsci2003.2298
  24. Smith OD, Simpson CE, Black MC, Besler BA. 1998. Registration of 'Tamrun 96' peanut. Crop Sci. 38:1403.
  25. Van Ooijen JW. 1999. LOD significance thresholds for QTL analysis in experimental populations of diploid species. Heredity 83: 613-624. https://doi.org/10.1038/sj.hdy.6886230
  26. Varshney RK, Bertioli DJ, Moretzsohn MC, Vadez V, Krishnamurthy L, Aruna R, et al. 2009. The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theor. Appl. Genet. 118: 729-739. https://doi.org/10.1007/s00122-008-0933-x
  27. Wang H, Pandey MK, Qiao L, Qin H, Culbreath AK, He G, et al. 2013. Genetic mapping and quantitative trait loci analysis for disease resistance using F2 and F5 generationbased genetic maps derived from 'Tifrunner' $\times$ 'GT-C20' in peanut. Plant Genome 6: 1-10.
  28. Wang S, Basten CJ, Zeng Z-B. 2012. Windows qtl cartographer v2.5_011. Program in Statistical Genetics, North Carolina State University. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm.
  29. Wehtje G, Walker RH, Patterson MG, Mcguire JA. 1984. Influence of twin rows on yield and weed control in peanuts. Peanut Science 11: 88-91. https://doi.org/10.3146/i0095-3679-11-2-10
  30. Wheeler TA, Choppakatla V, Porter DO, Schuster GL, Jr. BGM, Schubert AM. 2012. Irrigation rate and fungicide effects on peanut kernel damage, yield, and net return. Peanut Science 39: 88-94. https://doi.org/10.3146/PS09-019.1
  31. Whitaker TB, Dorner JW, Lamb M, Slate AB. 2005. The effect of sorting farmers' stock peanuts by size and color on partitioning aflatoxin into various shelled peanut grade sizes. Peanut Science 32: 103-118. https://doi.org/10.3146/0095-3679(2005)32[103:TEOSFS]2.0.CO;2
  32. Worland AJ, Law CN, Li WM. 1990. The location of genes depressing yield associated with the transfer of eyespot resistance from Aegilops ventricosa. IPSR & John Innes Institute, Norwich, UK. https://www.cabdirect.org/cabdirect/abstract/19911624132
  33. Wu Y, 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. https://doi.org/10.1371/journal.pgen.1000212