Sequence polymorphism of the waxy gene in waxy maize accessions and characterization of a new waxy allele

Abstract

Waxy maize has many excellent characteristics in terms of its nutritional and economic value. In recent decades, the waxy maize germplasm has increased dramatically as a result of different selection methods. We collected 200 waxy maize inbred accessions from different origins to study their genetic diversity and phylogenetic relationships, and to identify new waxy mutations. A simple sequence repeat (SSR) analysis revealed wide genetic diversity among the 200 waxy maize accessions. The maize accessions were clustered into three groups. We sequenced the waxy gene from the first to the 14th exon. Nucleotide variation analysis of 167 waxy maize and 14 flint maize lines revealed some nucleotide differences in the waxy gene among different waxy maize groups, and much narrower nucleotide diversity in waxy maize than in flint maize. In a phylogenetic analysis, waxy maize carrying the same mutation allele clustered together, and waxy maize carrying different mutation alleles distributed in different groups; waxy maize was intermixed with flint maize in each branch, and wx-D7 waxy maize separated significantly from waxy maize lines carrying wx-D10, wx-124 and wx-hAT mutant alleles. The wx-hAT was a new waxy mutation identified in this study. It consisted of a 2286-bp transposon inserted into the middle of exon three of the waxy gene. A PCR marker specific for the wx-hAT allele was developed. These results will be useful for the utilization and preservation of the waxy maize germplasm, and the PCR marker has potential uses in waxy maize breeding programs.

Starch biosynthesis in cereal endosperms: An updated review over the last decade

“…Since the cloning of the Wx gene in the 1980s, transgenic lines with various ACs have been established using antisense RNA, homologous recombination, and overexpression, and the effects of different ACs on starch physicochemical properties have been clarified ( Shimada et al., 1993 ; Terada et al., 2000 , 2002 ; Itoh et al., 2003 ; Liu et al., 2015a ). In recent years, diverse Wx alleles have been cloned in rice, maize, wheat, and barley ( Asare et al., 2012 ; Guzmán and Alvarez, 2016 ; Luo et al., 2020 ). Cloning of numerous null wx alleles in maize has enabled the convenient breeding of waxy maize with a unique chewing texture.…”

Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection

“…in waxy rice, resulting in the loss of GBSS function, which in turn causes the glutinous trait (Inukai et al, 2000;Wanchana et al, 2003;Teng et al, 2012). In parallel with waxy or glutinous rice, genetic identification and association mapping of the waxy gene in maize have been characterized in the recent decades (Huang et al, 2010;Hossain et al, 2019;Luo et al, 2020;Kim H. R. et al, 2021). The waxy gene of wild maize was located in chromosome 9 and comprised of 14 exons by 3.93 kb long (Luo et al, 2020), and has a higher genetic variation level than rice, representing most of the identified waxy mutations by insertions and deletions, such as wx-m9, wx-m5, wx-B3, wx-m1, and wx-B4 (Huang et al, 2010).…”

“…In parallel with waxy or glutinous rice, genetic identification and association mapping of the waxy gene in maize have been characterized in the recent decades (Huang et al, 2010;Hossain et al, 2019;Luo et al, 2020;Kim H. R. et al, 2021). The waxy gene of wild maize was located in chromosome 9 and comprised of 14 exons by 3.93 kb long (Luo et al, 2020), and has a higher genetic variation level than rice, representing most of the identified waxy mutations by insertions and deletions, such as wx-m9, wx-m5, wx-B3, wx-m1, and wx-B4 (Huang et al, 2010). Up to the recent updates, despite the presence of several mutant waxy alleles (>50) in maize (Huang et al, 2010), a low number (≥ 10) of waxy alleles (Wx a , Wx b , Wx in , Wx mp , Wx mq , Wx op/hp , Wx Iv , Wx mw , Wx Ia , and wx) have collectively been discovered in rice genome (Cai et al, 1998;Larkin and Park, 2003;Wanchana et al, 2003;Liu et al, 2009;Yang et al, 2013;Zhang et al, 2021;Zhou et al, 2021), and summarized for the identification of their specific polymorphic sites carrying different functional properties (Zhang et al, 2021).…”

“…Unlike the waxy locus of rice, maize has a higher genetic variation level within its waxy gene region (Huang et al, 2010). However, the genetic differentiation of a waxy gene region of both glutinous rice and maize was lower than those of non-glutinous ones (Olsen and Purugganan, 2002;Yamanaka et al, 2004;Fan et al, 2008Fan et al, , 2009Wei et al, 2012;Zheng et al, 2013;Sa et al, 2015;Luo et al, 2020).…”

Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE)

“…Despite the differences in specific expression patterns and protein locations of GBSSII and GBSSI [3], the two genes encoding these proteins share high sequence similarity with almost 66% identical deduced amino acid sequences in wheat [3] and about 70% homology at the nucleotide sequence level in rice [4]. However, several different functional alleles or haplotypes [12][13][14] have been identified in the waxy gene (GBSSI) region and are associated with amylose content in rice and many other crops, such as maize [15], wheat [16], barley [17], and cassava [18,19], but research on the functional properties of GBSSII gene in crops is limited, particularly in rice. A recent study reported novel GBSSII haplotypes in rice through genome-wide identification and genetic variation analyses [20], but additional evolutionary analyses on this gene have not been performed.…”