Quantitative trait loci analysis of seed oil content and composition of wild and cultivated soybean

Abstract

Background: Soybean oil is a major source of edible oil, and the domestication of wild soybean has resulted in significant changes in oil content and composition. Extensive efforts have been made to identify genetic loci that are related to soybean oil traits. The objective of this study was to identify quantitative trait loci (QTLs) related to soybean seed oil and compare the fatty acid composition between wild and cultivated soybean.

Results: Using the specific-locus amplified fragment sequencing (SLAF-seq) method, a total of 181 recombinant inbred lines (RILs) derived from a cross between wild soybean ZYD00463 (Glycine soja) and cultivated soybean WDD01514 (Glycine max) were genotyped. Finally, a high-density genetic linkage map comprising 11,398 single-nucleotide polymorphism (SNP) markers on 20 linkage groups (LGs) was constructed. Twenty-four stable QTLs for seed oil content and composition were identified by model-based composite interval mapping (CIM) across multiple environments. Among these QTLs, 23 overlapped with or were adjacent to previously reported QTLs. One QTL, qPA10_1 (5.94-9.98 Mb) on Chr. Ten is a novel locus for palmitic acid. In the intervals of stable QTLs, some interesting genes involved in lipid metabolism were detected.

Conclusions: We developed 181 RILs from a cross between wild soybean ZYD00463 and cultivated soybean WDD01514 and constructed a high-density genetic map using the SLAF-seq method. We identified 24 stable QTLs for seed oil content and compositions, which includes qPA10_1 on Chr. 10, a novel locus for palmitic acid. Some interesting genes in the QTL regions were also detected. Our study will provide useful information for scientists to learn about genetic variations in lipid metabolism between wild and cultivated soybean.

Keywords: Oil and fatty acids; QTL; SLAF-seq; Soybean (Glycine max).

Fig. 1

LOD curves on chromosomes for oil content and composition in four different environments. The x-axis indicates genetic position (cM) across the chromosome, the y-axis represents the LOD scores. Horizontal dashed line on the chart represents LOD threshold (3.6). Different environments are represented by different lines: red line (Wuhan in 2015), green line (Xuchang in 2015), yellow line (Wuhan in 2016) and blue line (Xuchang in 2016). LOD curves for oil content (a-d), palmitic acid (e-h), stearic acid (i), oleic acid (j and k), linoleic acid (l and m), and linolenic acid (n-p) in different environments. The arrow represents position of a QTL identified under a single environment, and the number is the genetic position (cM) of a QTL on chromosome

Fig. 2

Distribution of stable QTLs in this study and reported QTLs. The QTL regions are marked with bars. The reported QTLs are showed in black bar. The stable QTLs in this study are showed in different color bar. Red bar: oil content; green bar: palmitic acid; blue bar: stearic acid; yellow bar: oleic acid; pale red bar: linoleic acid; light green bar: linolenic acid