Construction of a high-density linkage map and QTL mapping for important agronomic traits in Stylosanthes guianensis (Aubl.) Sw.

Yan-Qiong Tang,Ya-Cao Ding,Xiang Ma,Zhu Liu,Jin-Ping Liu,Ze-Ting Ding,Zhi-Qiang Xia

doi:10.1038/s41598-019-40489-7

Yan-Qiong Tang, Ya-Cao Ding + Show 5 more

Open Access

https://doi.org/10.1038/s41598-019-40489-7

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Abstract

Stylosanthes guianensis (Aubl.) Sw. is an economically important pasture and forage legume in tropical regions of the world. Genetic improvement of the crop can be enhanced through marker-assisted breeding. However, neither single nucleotide polymorphism (SNP) markers nor SNP-based genetic linkage map has been previously reported. In this study, a high-quality genetic linkage map of 2572 SNP markers for S. guianensis is generated using amplified-fragment single nucleotide polymorphism and methylation (AFSM) approach. The genetic map has 10 linkage groups (LGs), which spanned 2226.6 cM, with an average genetic distance of 0.87 cM between adjacent markers. Genetic mapping of quantitative trait loci (QTLs) for important agronomic traits such as yield-related and nutritional or quality-related traits was performed using F2 progeny of a cross between a male-sterile female parent TPRC1979 and male parent TPRCR273 with contrasting phenotypes for morphological and physiological traits. A total of 30 QTLs for 8 yield-related traits and 18 QTLs for 4 nutritional or quality-related traits are mapped on the linkage map. Both the high-quality genetic linkage map and the QTL mapping for important agronomic traits described here will provide valuable genetic resources for marker-assisted selection for S. guianensis.

Highlights

Important agronomic traits are generally inherited in a quantitative way, and marker-assisted selection (MAS) is very useful for tracing elite alleles that control these important, complex traits accelerating the breeding process[1]
Excluding the unlinked and co-segregated single nucleotide polymorphism (SNP) markers, we constructed the linkage map with 2572 markers distributed across 10 linkage groups (LGs)
Construction of a high-density genetic map can provide a valuable resource for understanding the basis of important complex agronomic traits in S. guianensis

Summary

Introduction

Important agronomic traits are generally inherited in a quantitative way, and marker-assisted selection (MAS) is very useful for tracing elite alleles that control these important, complex traits accelerating the breeding process[1]. Simple sequence repeat (SSR) markers are unqualified for the construction of high-density genetic linkage map because of their limited number and coverage and lacking sequence information, despite having advantages over aforementioned marker types such as co-dominant inheritance, locus specificity and reproducibility[3]. Several NGS-based approaches have been developed to identify SNPs, such as restriction site associated DNA sequencing (RAD-seq)[9], genotyping-by-sequencing (GBS)10, 2b-RAD11, specific length amplified fragment sequencing (SLAF-seq)[12], double digest RAD (ddRAD)[13] and amplified-fragment single nucleotide www.nature.com/scientificreports/. Www.nature.com/scientificreports polymorphism and methylation (AFSM)[14] These technologies have been successfully applied to construct high-resolution genetic linkage maps for many important crops[15,16,17,18,19]. Due to the non-availability of co-dominant markers of high level polymorphism, high-density linkage map for S. guianensis has not been generated successfully

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Conclusion