A QTL associated with high seed coat cracking rate of a leading Japanese soybean variety

Abstract

Seed coat cracking in soybeans [Glycine max (L). Merr.] leads to commercial and agronomic losses. The Japanese elite soybean cultivar 'Fukuyutaka' is often used as a parent for breeding, but its high rate of seed coat cracking is an obstacle to its further use in breeding programs. To establish a DNA marker-assisted selection system for seed coat cracking, genetic factors related to high rates of seed coat cracking were surveyed, and a quantitative trait locus (QTL) with a stable effect on seed coat cracking in both years of a two-year replication experiment was detected on chromosome 20. Comparison of a set of near-isogenic lines (NILs) around this locus verified that the presence of the 'Fukuyutaka' allele significantly increased seed coat cracking in the kernel. The locus is located in a genomic region spanning 3.2 Mb. Marker-assisted selection for the locus will improve the selection efficiency of 'Fukuyutaka'-derived breeding populations.

High-density linkage map reveals QTL for Type-I seed coat cracking in RIL population of soybean [Glycine max (L.) Merr.]

“…The SCC of RIL population showed transgressive segregation, especially over the susceptible parent because the resistant parent showed small variance (2.33), whereas the susceptible parent showed large variance (49.92). Similar results of right-skewed distribution were also found in previous studies (Oyoo et al 2010;Ha et al 2012;Saruta et al 2019).…”

“…The average distance between SNP markers, in this study, was 0.7 cM, which was relatively of higher density compared to previous QTL studies for SCC (Oyoo et al 2010;Ha et al 2012;Saruta et al 2019). Construction of the high-density linkage map is important for precise mapping of QTLs and their potential application in breeding programs.…”

“…qSC19-1 and qSC19-2 were found to cover the physical location of qSCC19 (Ha et al 2012), and located 2 Mb far from E3 locus (Mao et al 2017). Similarly, qSC20 co-localized with qSCC20 (Ha et al 2012;Saruta et al 2019). These results showed that the SCC variation found in the RIL population was not directly related to the maturity loci E3 and E10, and the association of SCC with E4 was not also clear (Molnar et al 2003).…”

“…Out of the 10 QTLs, three QTLs (qSCC2-1, qSCC9, and qSCC20) were identified in more than two environments. Saruta et al (2019) identified the QTL qScr20-1 on chromosome 20 (I) using 172 RILs genotyped with 264 SSR markers.…”

Characterization of the Common Genetic Basis Underlying Seed Hilum Size, Yield, and Quality Traits in Soybean

“…Numerous studies have been conducted with traits that are readily visible on soybean seeds, such as seed coat color, hilum color, and coat cracking, and which can have considerable impacts on commercial value ( Oyoo et al, 2010 ; Guo and Qiu, 2013 ; Sonah et al, 2015 ; Cho et al, 2017 ; Saruta et al, 2019 ). Interestingly, some of these visual traits are also highly correlated with seed yield and/or quality traits.…”