Relationship between Mutations of the Pectin Methylesterase Gene in Soybean and the Hardness of Cooked Beans

Abstract

Hardness of cooked soybeans [Glycine max (L). Merr.] is an important attribute in food processing. We found one candidate gene, Glyma03g03360, to be associated with the hardness of cotyledons of cooked soybeans, based on a quantitative trait locus and fine-scale mapping analyses using a recombinant inbred line population developed from a cross between two Japanese cultivars, "Natto-shoryu" and "Hyoukei-kuro 3". Analysis of the DNA sequence of Glyma03g03360, a pectin methylesterase gene homologue, revealed three patterns of mutations, two of which result in truncated proteins and one of which results in an amino acid substitution. The truncated proteins are presumed to lack the enzymatic activity of Glyma03g03360. We classified 24 cultivars into four groups based on the sequence of Glyma03g03360. The texture analysis using the 22 cultivars grown in different locations indicated that protein truncation of Glyma03g03360 resulted in softer cotyledons of cooked soybeans, which was further confirmed by texture analysis performed using F2 populations of a cross between "Enrei" and "LD00-3309", and between "Satonohohoemi" and "Sakukei 98". A positive correlation between hardness and calcium content implies the possible effect of calcium binding to pectins on the hardness of cooked soybean cotyledons.

DNA marker-assisted evaluation of cooked bean hardness of three soybean progeny lines

“…A stop codon is inserted in the B and Bʹ genotypes, resulting in amino-acid sequences lacking amino acids that are catalytically important ( Bosch et al 2005 , Jimenez-Lopez et al 2012 ). The cooked bean hardness of soybean carrying the A or Aʹ genotypes was found to be significantly higher than that of soybean carrying the B or Bʹ genotypes ( Toda et al 2015 ), which supports the suggested mechanism of softening tissues by the β-elimination of pectins.…”

“…Previously, we demonstrated that the hardness of cooked soybeans is affected by genetic factors, and Glyma03g03360 polymorphism, which was recently renamed as Glyma.03g028900 , is associated with the cooked bean hardness ( Hirata et al 2014 , Toda et al 2015 ). Glyma03g03360 encodes a pectin methylesterase (PME) of 490 amino acids in length ( Toda et al 2015 , SoyBase, ). Pectin, which is a major component of primary cell walls and the middle lamella, is mainly constituted of linear chains of 1,4-linked alpha-D-galacturonic acid units.…”

“…β-elimination of pectins is primarily responsible for heat degradation at pH 6.1, and the rate of the β-eliminative cleavage of prepared pectin is dependent on the degree of esterification ( Sajjaanantakul et al 1989 ). Glyma03g03360 is expressed in the cotyledon and seed coat during the later stage of seed development ( Toda et al 2015 ), which probably decreases the degree of esterification in those tissues, resulting in harder cooked beans.…”

“…DNA marker-assisted selection (MAS) has been successfully incorporated into soybean breeding programs to select diverse traits such as soybean pod dehiscence and maturity time ( Suzuki et al 2010 , Yamada et al 2012 ). Cooked bean hardness can also be evaluated by DNA markers, because our previous studies indicated a primary effect of Glyma03g03360 on this trait ( Hirata et al 2014 , Toda et al 2015 ).…”

Soybean domestication: the origin, genetic architecture and molecular bases

“…It is therefore possible that different types of selection may have acted on seed hardness-related traits in early domestication and in modern soybean improvement. Concerning the hardness of cooked seeds, a potential causal gene of a major locus, qHbs3-1, was identified as a pectin methylesterase homolog (Toda et al, 2015). Identification of additional genes underlying seed permeability and seed hardness and further evolutionary studies at New Phytologist (2017)…”