Qian Zhu, Diana M. Escamilla, Xingbo Wu, Qijian Song, Song Li, M. Luciana Rosso, Nilanka Lord, Futi Xie & Bo Zhang

Theoretical and Applied Genetics November 2020; vol. 133:3165–3176.

Key message

Two major QTLs associated with low seed coat deficiency of soybean seeds were identified in two biparental populations, and three SNP markers were validated to assist low-SCD natto soybean breeding selection.

Abstract

Soybean seed coat deficiency (SCD), known as seed coat cracking during soaking in the natto production process, is problematic because split or broken beans clog production lines and increases production costs. Development of natto soybean cultivars with low SCD is crucial to support the growth of the natto industry. Unfortunately, information on the genetic control of SCD in soybean, which is desperately needed to facilitate breeding selection, remains sparse. In this study, two F₂ populations derived from V11-0883 × V12-1626 (Pop 1) and V11-0883 × V12-1885 (Pop 2) were developed and genotyped with BARCSoySNP6K Beadchips and F₂-derived lines were evaluated for SCD in three consecutive years (2016–2018) in order to identify quantitative trait loci (QTLs) associated with low SCD in soybean. A total of 17 QTLs underlying SCD were identified in two populations. Among these, two major and stable QTLs, qSCD15 on chromosome 15 and qSCD20 on chromosome 20, were detected across multiple years. These QTLs explained up to 30.3% of the phenotypic variation for SCD in Pop 1 and 6.1% in Pop 2 across years. Three SNP markers associated with the qSCD20 were validated in additional four biparental populations. The average selection efficiency of low-SCD soybean was 77% based on two tightly linked markers, Gm20_34626867 and Gm20_34942502, and 64% based on the marker Gm20_35625615. The novel and stable QTLs identified in this study will facilitate elucidation of the genetic mechanism controlling SCD in soybean, and the markers will significantly accelerate breeding for low-SCD soybean through marker-assisted selection.

See: https://link.springer.com/article/10.1007/s00122-020-03662-5

 Figure 2 & 3:

Above: Mapping for seed coat deficiency (SCD) in the Pop 1 (V11-0883 × V12-1626) in individual and across years (AVE). QTL nomenclature is in the form of qTraitChr. Colored intervals refer to the mapped QTLs detected by CIM and/or IM in different environments, the curves indicate the physical position of markers against LOD score detected on chromosomes, and lines with different colors represent different environments.

Belowe: Mapping for seed coat deficiency (SCD) in the Pop 2 (V11-0883 × V12-1885) in individual and across years (AVE). QTL nomenclature is in the form of qTraitChr. Colored intervals refer to the mapped QTLs detected by CIM and/or IM in different environments; the curves indicate the physical position of markers against LOD score detected on chromosomes, and lines with different colors represent different environments