Wx, the Ancestral Allele of Rice Waxy Gene

Abstract

In rice grains, the Waxy (Wx) gene is responsible for the synthesis of amylose, the most important determinant for eating and cooking quality. The effects of several Wx alleles on amylose content and the taste of cooked rice have been elucidated. However, the relationship between artificial selection and the evolution of various Wx alleles as well as their distribution remain unclear. Here we report the identification of an ancestral allele, Wx lv , which dramatically affects the mouthfeel of rice grains by modulating the size of amylose molecules. We demonstrated that Wx lv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wx b , Wx a , and Wx in ) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wx lv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.

Natural Polymorphisms in Arabidopsis Result in Wide Variation or Loss of the Amylose Component of Starch

“…2). Amylose-free varieties of crops have been cultivated for centuries, but these mutants have been maintained in several crop species by positive selection for the desirable properties of amylose-free starch and flour (Olsen and Purugganan, 2002;Stamp et al, 2016;Zhang et al, 2019). Thus, the discovery of wild accessions of a noncultivated plant species that contain no or very low amylose is surprising.…”

A Silent Exonic Mutation in a Rice Integrin-α FG-GAP Repeat-Containing Gene Causes Male-Sterility by Affecting mRNA Splicing

“…For example, in rice, the Waxy (Wx) gene encodes a granule-bound starch synthase, which regulates the amylose content and determines the eating and cooking quality [44]. In indica rice that contains high endosperm amylose level, Wx with a normal sequence has correct mRNA transcripts, whereas the Wx in japonica rice shows a single base change at the 5 splice site (splice donor site) of the first intron, representing a larger mRNA with retention of the first intron, which reduces the levels of Wx protein and endosperm amylose [44][45][46]. A mutation at the 3 splice site (splice acceptor site) of a intron in MUTANT snc1-ENHANCING (MUSE), an Arabidopsis RNA polymerase III subunit, gives rise to intronic retention and partial loss-of-function of MUSE, leading to pleiotropic defects in vegetative development [47].…”

Creating novel Wx alleles with fine‐tuned amylose levels and improved grain quality in rice by promoter editing using CRISPR/Cas9 system

“…In rice, the Waxy (Wx) gene encoding GBSSI (granule-bound starch synthase I) controls amylose synthesis in endosperm and is the primary factor influencing grain eating and cooking quality (ECQ) (Sano, 1984;Tian et al, 2009). The natural allelic variations within the Wx locus are the main cause of the broad diversity of amylose content (AC) and ECQ in modern rice (Zhang et al, 2019). Our recent study revealed a high-to-low AC selection trend globally in the course of rice domestication (Zhang et al, 2019).…”

“…The natural allelic variations within the Wx locus are the main cause of the broad diversity of amylose content (AC) and ECQ in modern rice (Zhang et al, 2019). Our recent study revealed a high-to-low AC selection trend globally in the course of rice domestication (Zhang et al, 2019). In recent decades, there have been advances in modulating AC and improving ECQ in both indica and japonica rice using certain Wx alleles, particularly Wx b and Wx in with low-tointermediate AC (Lau et al, 2016).…”

“…Excluding a slight decrease in kernel weight, all the lines had no significant differences in major agronomic traits and grain phenotype ( Figure 1d) compared with the wild type. First, the transcript abundance of six novel Wx alleles was compared with that in Nipponbare (Wx b ) and its near-isogenic line (NIL) (wx) carrying the null wx allele (Zhang et al, 2019). As there will be Wx precursor mRNA (pre-mRNA) present due to the G-to-T variation in the splice site of intron 1 of the Wx b allele (Cai et al, 1998), three pairs of primers (Figure 1a,e) were designed to evaluate the abundance of pre-mRNA, mature mRNA and total mRNA of Wx, respectively.…”