Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds ( Glycine ma
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ORIGINAL ARTICLE
Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds (Glycine max L.) Qian Zhu1,2 · Diana M. Escamilla3 · Xingbo Wu1 · Qijian Song4 · Song Li1 · M. Luciana Rosso1 · Nilanka Lord1 · Futi Xie2 · Bo Zhang1 Received: 18 February 2020 / Accepted: 3 August 2020 © The Author(s) 2020
Abstract 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 F 2 populations derived from V11-0883 × V12-1626 (Pop 1) and V11-0883 × V12-1885 (Pop 2) were developed and genotyped with BARCSoySNP6K Beadchips and F 2-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.
Introduction
Communicated by Brian Diers. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03662-5) contains supplementary material, which is available to authorized users. * Bo Zhang [email protected] 1
School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
2
College of Agronomy, Shenyang Agricultural University, Shenyang 110866, People’s Republic of China
3
Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
4
Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD 20705, USA
Because of its high content of protein, fiber, amino acids, and isoflavones, soybean (Glycine max L. Merr.) has become increasingly appealing for human consumption as a nutritio
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