Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut (Arachis hypogaea L.).

Li Huang,Manish K Pandey,Xiaojing Zhou,Xiaoping Ren,Yuning Chen,Yongqing Jiao,Yong Lei,Huaiyong Luo,Bei Wu,Xinping Li,Rajeev K Varshney,Huifang Jiang,Weigang Chen,Boshou Liao

doi:10.1038/srep39478

Abstract

Plant height is one of the most important architecture traits in crop plants. In peanut, the genetic basis of plant height remains ambiguous. In this context, we genotyped a recombinant inbred line (RIL) population with 140 individuals developed from a cross between two peanut varieties varying in plant height, Zhonghua 10 and ICG 12625. Genotyping data was generated for 1,175 SSR and 42 transposon polymorphic markers and a high-density genetic linkage map was constructed with 1,219 mapped loci covering total map length of 2,038.75 cM i.e., accounted for nearly 80% of the peanut genome. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data for three environments identified 8 negative-effect QTLs and 10 positive-effect QTLs for plant height. Among these QTLs, 8 QTLs had a large contribution to plant height that explained ≥10% phenotypic variation. Two major-effect consensus QTLs namely cqPHA4a and cqPHA4b were identified with stable performance across three environments. Further, the allelic recombination of detected QTLs proved the existence of the phenomenon of transgressive segregation for plant height in the RIL population. Therefore, this study not only successfully reported a high-density genetic linkage map of peanut and identified genomic region controlling plant height but also opens opportunities for further gene discovery and molecular breeding for plant height in peanut.

Highlights

Max peanut is too dwarf or too high, the combine harvesters could miss some pods or make some peanut straw and pods mixed together
Thousands of Simple sequence repeat (SSR) markers have been developed in peanut from complementary DNAs, SSR-enriched genomic DNA libraries, and BAC-ends[25,32,33,34,35,36,37], which greatly accelerated the construction of genetic map and Quantitative trait locus (QTL) analysis in peanut[21,23,24,25,27,28,29,38,39,40]
Since the polymorphism of SSRs in a specific population largely depended on the genetic diversity between the parents of an experimental population, several such efforts were required to make available large number of SSRs in the public domain for genetic and QTL mapping studies

Summary

Introduction

Max peanut is too dwarf or too high, the combine harvesters could miss some pods or make some peanut straw and pods mixed together. Simple sequence repeat (SSR) markers have been the choice of genetic markers and were used for developing genetic maps for cultivated peanuts which in turn facilitated several QTL mapping studies in peanut using F2 and recombinant inbred lines (RIL) populations. Many of these QTLs were detected for drought tolerance[17,18,19], resistance to biotic stresses such as late leaf spot, rust and bacterial wilt resistance[20,21,22], pod- and seed-related traits[23,24,25] and quality traits[23,26,27,28]. The present study reports the development of high-density genetic linkage map for cultivated peanut; getting insights on the genetic basis of plant height in peanut and genome-wide identification of QTLs controlling plant height in peanut using the RIL population

Methods

Results

Conclusion