Genetic map construction and QTL analysis of leaf-related traits in soybean under monoculture and relay intercropping

Dai-Ling Liu,Chun-Yan Liu,Wei-Guo Liu,Feng Yang,Yue-Hui She,Wen-Yu Yang,Si-Wei Chen,Jun-Bo Du,Xin-Chun Liu,Xiao-Ling Wu

doi:10.1038/s41598-019-39110-8

Dai-Ling Liu, Chun-Yan Liu + Show 8 more

Open Access

https://doi.org/10.1038/s41598-019-39110-8

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Abstract

Soybean (Glycine max L.) is an important food and oil crop widely planted by intercropping in southwest China. The shade caused by intercropping changes plant growth traits, such as soybean leaf and dry mass, thereby reducing yields. To improve the yield and elucidate the genetic mechanism of the leaf-related traits in intercropped soybeans, we measured the F6:7–8 recombinant inbred lines (RILs) derived from the cross of ‘Nandou 12’ and ‘Jiuyuehuang’ for six leaf-related traits under monoculture and relay intercropping in 2015 and 2016. We found 6366 single-nucleotide polymorphisms (SNPs) markers that covered the whole genome of soybean distributed in 20 linkage groups, which spanned 2818.67 cM with an average interval of 0.44 cM between adjacent markers. Nineteen quantitative trait loci (QTLs) were detected in two environments in 2 years. Three candidate genes associated to leaf-related traits were found according to gene expression and GO enrichment analyses. These results revealed the susceptibility of leaf phenotype to shading and helped elucidate the mechanisms that control leaf-related traits.

Highlights

Soybean (Glycine max L.) is an important crop with a high protein and oil content, and is widely used for food and feed and chemical industry
The results of variance analysis indicated the significant variation in compound leaf number (CLN), total leaflet area (TLA), specific leaflet area (SLA), specific leaflet weight (SLW), and leaflet dry weight (LDW) except leaflet dry weight ratio (LDWR) between monoculture and relay intercropping
SLA in relay intercropping was significantly higher than that in monoculture. These results revealed the susceptibility of leaf phenotype to shading

Summary

Introduction

Soybean (Glycine max L.) is an important crop with a high protein and oil content, and is widely used for food and feed and chemical industry. Maize-soybean relay strip intercropping remarkably increases the planting area and production of soybean and maintains the yield of maize[1,2] In this planting pattern, soybean is subjected to shading at the co-growth stage. More than 88 quantitative trait loci (QTLs) associated with soybean leaf-related traits have been reported. We analyzed the leaf phenotype under monoculture (M) and relay intercropping (RI), developed a high-density soybean molecular genetic map by using a specific-locus amplified fragment sequencing (SLAF-seq) technology, and identified the QTL for leaf-related traits by utilizing RILs derived from ‘Nandou 12’ and ‘Jiuyuehuang’, and determined the main effect of QTLs and select candidate genes that may influence the leaf phenotype through Gene Ontology (GO) enrichment analysis

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Results

Conclusion