Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds (Glycine max L.)

Authors: ZHU, QIAN - Virginia Tech; ESCAMILLA, DIANA - Purdue University; WU, XINGBO - Virginia Tech; Song, Qijian; LI, SONG - Virginia Tech; ROSSO, LUCIANA - Virginia Tech; LORD, NILANKA - Virginia Tech; XIE, FUTI - Shenyang Agricultural University; ZHANG, BO - Virginia Tech

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/3/2020
Publication Date: 8/26/2020
Citation: Zhu, Q., Escamilla, D.M., Wu, X., Song, Q., Li, S., Rosso, L., Lord, N., Xie, F., Zhang, B. 2020. Identification and validation of major QTLs associated with low seed coat deficiency of natto soybean seeds (Glycine max L.). Theoretical and Applied Genetics. 133(1):3165-3176. https://doi.org/10.1007/s00122-020-03662-5.
DOI: https://doi.org/10.1007/s00122-020-03662-5

Interpretive Summary: Natto is a traditional Japanese fermented soyfood well known for its unique flavor and stickiness. The U.S. has been the largest soybean exporter to Japan for natto production since the early 1990s. The high demand of natto consumption in Japan not only results in a great international soybean market, but also requires U.S. growers to provide high quality food-grade soybean to meet manufacturing requirements. Although small seed size, round shape and yellow coat color are preferred for natto production, a low cracking ratio during processing is most important to manufacturers because cracked seeds will affect natto appearance and clog production lines. Hence, breeding soybean varieties with low seed coat deficiency (SCD) is desirable. In this study, we detected two gene regions that were associated with SCD in soybean. We also developed three markers to tag the gene regions and demonstrated that the markers had a high selection efficiency of low SCD during breeding. The results described in this study will be useful for soybean breeders and food scientists to produce high quality natto soybeans with genetically superior process quality to meet consumer and manufacturer needs.

Technical 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 bi-parental 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.