花生百果重、百仁重和出仁率多效性QTL发掘和KASP标记开发

doi:10.1016/j.jia.2024.06.013

摘要/Abstract

摘要：

高产一直是花生育种的首要目标。百果重(HPW)、百仁重(HSW)和出仁率(SP)是花生产量的重要组成部分。本研究旨在通过对“四粒红”（多粒型）与“冀农黑3号”（普通型）杂交的重组自交系(RILs)进行重测序，构建高密度连锁图谱。该图谱由4499个bin组成，分布在20条染色体上，全长1712.32 cM，平均标记间距离为0.38 cM。在3种环境中共鉴定出46个QTL位点。其中，主效QTL位点qHPW5.2、qHPW18.1、qSP7.1、qSP8.1、qSP8.2、qSP18.1和qSP18.2的表型变异解释分别为12.04、11.41、16.53、24.17、10.49、10.82和29.89%。的14个QTL在多个环境中被检测到，认为是稳定的QTL。1个QTL (qHPW7、qHSW7.1、qSP7)与3个性状均相关，对HPW、HSW和SP的表型变异解释分别为8.91、9.04和16.53%。利用美国微核心种质进行全基因组关联来验证QTL定位的准确性。在两种环境中，共检测到115个SNP与百果重、百仁重和出仁率显著相关。6个SNP与2个性状同时相关，平均解释13.84%的表型变异。结合两个定位群体，关联分析群体中在 7号染色体上与SP显著相关的SNP，AX-176802178，同时位于RIL群体主效QTL qSP7置信区间内。此外，还开发了3个KASP标记，并在花生农家种和品种中进行了验证。这些QTL为了解花生HPW、HSW和SP的遗传基础提供了有价值的见解，并为花生标记辅助育种提供有用的分子标记。

Abstract:

High yield has always been the primary objective of peanut breeding. 100-pod weight (HPW), 100-seed weight (HSW), and shelling percentage (SP), are crucial components of peanut yield. This study aimed to construct a high-density linkage map by resequencing the recombined inbred lines (RILs) derived from a cross between “Silihong” (A. hypogaea var. fastigiate) and “Jinonghei 3” (A. hypogaea var. hypogaea). The map consisted of 4,499 bins spread across 20 chromosomes, totaling 1712.32 cM in length with an average inter-marker distance of 0.38 cM. A total of 46 quantitative trait loci (QTLs) were identified across three environments. The major QTLs, including qHPW5.2, qHPW18.1, qSP7.1, qSP8.1, qSP8.2, qSP18.1, and qSP18.2, exhibited PVE (phenotypic variation explained) of 12.04, 11.41, 16.53, 24.17, 10.49, 10.82, and 29.89%, respectively. Fourteen QTLs identified across multiple environments were considered stable. One QTL (qHPW7, qHSW7.1, qSP7) was associated with all three traits, with the PVE value of 8.91, 9.04, and 16.53% for HPW, HSW, and SP, respectively. The genome-wide association study was conducted using the US mini-core collection to validate the accuracy of QTL mapping. Across two environments, 115 single-nucleotide polymorphisms (SNPs) were significantly associated with HPW, HSW, and SP in the association panel. Six SNPs were associated with two traits, explaining an average phenotypic variation of 13.84%. Combining the two mapping populations, AX-176802178, detected on chromosome 7 in the association panel, which controlled SP, was located within the QTL qSP7 confidence interval defined by the RILs. Moreover, three KASP markers were developed and validated in peanut landraces and varieties. These QTLs might offer valuable insights for understanding the genetic basis of HPW, HSW, and SP and provide useful molecular markers for marker-assisted breeding in peanuts.

Key words: Arachis hypogaea L. , GWAS , , KASP , , QTL mapping , , shelling percentage

. 花生百果重、百仁重和出仁率多效性QTL发掘和KASP标记开发[J]. Journal of Integrative Agriculture, DOI: 10.1016/j.jia.2024.06.013.

Xiukun Li, Jing Hao, Hongtao Deng, Shunli Cui, Li Li, Mingyu Hou, Yingru Liu, Lifeng Liu. Identification of a pleiotropic QTL and development KASP markers for HPW, HSW, and SP in peanut[J]. Journal of Integrative Agriculture, DOI: 10.1016/j.jia.2024.06.013.

参考文献

Bertioli D J, Cannon S B, Froenicke L, Huang G, Farmer A D, Cannon E K, Liu X, Gao D, Clevenger J, Dash S, Ren L, Moretzsohn M C, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth C E, Umale P, Araujo A C, et al. 2016. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genetics, 48, 438-446.

Bertioli D J, Jenkins J, Clevenger J, Dudchenko O, Gao D, Seijo G, Leal-Bertioli S C M, Ren L, Farmer A D, Pandey M K, Samoluk S S, Abernathy B, Agarwal G, Ballén-Taborda C, Cameron C, Campbell J, Chavarro C, Chitikineni A, Chu Y, Dash S, et al. 2019. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics, 51, 877-884.

Carter E T , Rowland D L, Tillman B L, Erickson J E, Grey T L, Gillett-Kaufman J L, Clark M W. 2017. Pod maturity in the shelling process. Peanut Science, 44, 26–34.

Chavarro C, Chu Y, Holbrook C, Isleib T, Bertioli D, Hovav R, Butts C, Lamb M, Sorensen R, Jackson S A, Peggy O-A. 2020. Pod and seed trait qtl identification to assist breeding for peanut market preferences. G3 (Bethesda), 10, 2297-2315.

Chen C Y, Barkley N A, Wang M L, Holbrook C C, Dang P M. 2014. Registration of purified accessions for the U.S. peanut mini-core germplasm collection. Journal of Plant Registrations, 8, 77-85.

Chen Z L, Wang B B, Dong X M, Liu H, Ren L H. 2014. An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population. BMC Genomics, 15, 433.

Chu Y, Chee P, Isleib T G, Holbrook C C, Ozias-Akins P. 2020. Major seed size QTL on chromosome A05 of peanut (Arachis hypogaea) is conserved in the US mini core germplasm collection. Molecular Breeding, 40, 6.

Dash S, Cannon E K S, Kalberer S R, Farmer A D, Cannon S B. 2016. Peanutbase and other bioinformatic resources for peanut. Peanuts, AOCS Press, 241-252.

Gangurde S S, Wang H, Yaduru S, Pandey M K, Fountain J C, Chu Y, Isleib T, Holbrook C C, Xavier A, Culbreath A K, Ozias-Akins P, Varshney R K, Guo B. 2020. Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea). Plant Biotechnology Journal, 18, 1457-1471.

Holland J B. 2007. Genetic architecture of complex traits in plants. Current Opinion in Plant Biology, 10, 156-161.

Huang L, He H, Chen W, Ren X, Chen Y, Zhou X, Xia Y, Wang X, Jiang X, Liao B. 2015. Quantitative trait locus analysis of agronomic and quality-related traits in cultivated peanut (Arachis hypogaea L.). Theoretical and Applied Genetics, 128, 1103–1115.

Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T. 2009. High-throughput genotyping by whole-genome resequencing. Genome Research, 19, 1068-1076.

Jiang H. 2006. Descriptors and data standard for peanut (Arachis spp.). China Agriculture Press, 11-36. (in Chinese)

Kai W, Li M, Hakon H. 2010. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 16, e164.

Kunta S, Chu Y, Levy Y, Harel A, Hovav R. 2022. Identification of a major locus for flowering pattern sheds light on plant architecture diversification in cultivated Peanut. Theoretical and Applied Genetics, 135, 1767-1777.

Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. Genome project data processing S: The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.

Li L, Cui S, Dang P, Yang X, Wei X, Chen K, Liu L, Chen C Y. 2022. GWAS and bulked segregant analysis reveal the Loci controlling growth habit-related traits in cultivated peanut (Arachis hypogaea L.). BMC Genomics, 23, 1-13.

Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. 2009a. SNP detection for massively parallel whole-genome resequencing. Genome Research, 19, 1124-1132.

Li R, Yu C, Lam T W, Yiu S M, Kristiansen K, Wang J. 2009b. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.

Li W, Liu N, Huang L, Chen Y, Guo J, Yu B, Luo H, Zhou X, Huai D, Chen W, Yan L, Wang X, Lei Y, Liao B, Jiang H. 2022. Stable major QTL on chromosomes A07 and A08 increase shelling percentage in peanut (Arachis hypogaea L.). The Crop Journal, 10, 820-829.

Lu Y, Zhang S, Shah T, Xie C, Hao Z, Li X, Farkhari M, Ribaut J M, Cao M, Rong T. 2010. Joint linkage-linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. Proceedings of the National Academy of Sciences of the United States of America, 107, 19585-19590.

Lucia R, Gomes F, Celis A, Lopes A. 2005. Correlations and path analysis in peanut. Crop Breeding & Applied Biotechnology, 5, 105-110.

Luo H, Guo J, Ren X, Chen W, Huang L, Zhou X, Chen Y, Liu N, Xiong F, Lei Y, Liao B, Jiang H. 2018. Chromosomes A07 and A05 associated with stable and major QTLs for pod weight and size in cultivated peanut (Arachis hypogaea L.). Theoretical and Applied Genetics, 131, 267-282.

Luo H, Pandey M K, Khan A W, Guo J, Wu B, Cai Y, Huang L, Zhou X, Chen Y, Chen W, Liu N, Lei Y, Liao B, Varshney R K, Jiang H. 2019. Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.). Plant Biotechnology Journal, 17, 1248-1260.

Luo H, Xu Z, Li Z, Li X, Lv J, Ren X, Huang L, Zhou X, Chen Y, Yu J. 2017. Development of SSR markers and identification of major quantitative trait loci controlling shelling percentage in cultivated peanut (Arachis hypogaea L.). Theoretical and Applied Genetics, 130, 1635–1648.

Meng X, Zhang J, Cui S, Chen C Y, Mu G, Hou M, Yang X, Liu L. 2021. QTL mapping and QTL × Environment interaction analysis of pod and seed related traits in cultivated peanut (Arachis hypogaea L.). Acta Agronomica Sinica, 47, 1874-1890. (in Chinese)

Meuwissen T, Goddard M. 2010. Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics, 185, 622-623.

Pawan K, Pandey M K, Wang H, Feng S, Qiao L, Culbreath A K, Sandip K, Wang J, Corley H C, Zhuang W. 2016. Mapping quantitative trait loci of resistance to tomato spotted wilt virus and leaf spots in a recombinant inbred line population of peanut (Arachis hypogaea L.) from SunOleic 97R and NC94022. PLoS ONE, 11, e0158452.

Ravi K, Vadez V, Isobe S, Mir R R, Guo Y, Nigam S N, Gowda M, Radhakrishnan T, Bertioli D J, Knapp S J. 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.). Theoretical and Applied Genetics, 122, 1119-1132.

Robledo G, Lavia G I, Seijo G. 2009. Species relations among wild Arachis species with the A genome as revealed by FISH mapping of rDNA loci and heterochromatin detection. Theoretical and Applied Genetics, 118, 1295-1307.

Verhertbruggen Y, Bouder A, Vigouroux J, Alvarado C, Geairon A, Guillon F, Wilkinson M D, Stritt F, Pauly M, Lee M Y, Mortimer J C, Scheller H V, Mitchell R A C, Voiniciuc C, Saulnier L, Chateigner-Boutin A L. 2021. The TaCslA12 gene expressed in the wheat grain endosperm synthesizes wheat-like mannan when expressed in yeast and Arabidopsis. Plant Science, 302, 110693.

Wang L, Yang X, Cui S, Mu G, Sun X, Liu L, Li Z. 2019. QTL mapping and QTL × environment interaction analysis of multi-seed pod in cultivated peanut (Arachis hypogaea L.). The Crop Journal, 7, 249-260.

Wang Z, Yan L, Chen Y, Wang X, Huai D, Kang Y, Jiang H, Liu K, Lei Y, Liao B. 2022. Detection of a major QTL and development of KASP markers for seed weight by combining QTL-seq, QTL-mapping and RNA-seq in peanut. Theoretical and Applied Genetics, 135, 1779-1795.

Zhang C, Zhou Z, Yong H, Zhang X, Hao Z, Zhang F, Li M, Zhang D, Li X, Wang Z. 2017. Analysis of the genetic architecture of maize ear and grain morphological traits by combined linkage and association mapping. Theoretical and Applied Genetics, 130, 1011-1029.

Zhang S, Hu X, Miao H, Chu Y, Cui F, Yang W, Wang C, Shen Y, Xu T, Zhao L, Zhang J, Chen J. 2019. QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut (Arachis hypogaea L.). BMC Plant Biology, 19, 537.

Zhuang W, Chen H, Yang M, Wang J, Pandey M K, Zhang C, Chang W C, Zhang L, Zhang X, Tang R, Garg V, Wang X, Tang H, Chow C N, Wang J, Deng Y, Wang D, Khan A W, Yang Q, Cai T, et al. 2019. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature Genetics, 51, 865-876.

Zou C, Wang P, Xu Y. 2016. Bulked sample analysis in genetics, genomics and crop improvement. Plant Biotechnology Journal, 14, 1941-1955.