A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency

Abstract

In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy (Wx) locus. Here we identified a rare Wx allele, Wxmw, which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wxmw may have derived from recombination between two important natural Wx alleles, Wxin and Wxb. We validated the effects of Wxmw on rice grain quality using both transgenic lines and near‐isogenic lines (NILs). When introgressed into the japonica Nipponbare (NIP) background, Wxmw resulted in a moderate AC that was intermediate between that of NILs carrying the Wxb allele and NILs with the Wxmp allele. Notably, mature grains of NILs fixed for Wxmw had an improved transparent endosperm relative to soft rice. Further, we introduced Wxmw into a high‐yielding japonica cultivar via molecular marker‐assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wxmw is a promising allele to improve grain quality, especially ECQ and grain transparency of high‐yielding japonica cultivars, in rice breeding programs.

Novel Wx alleles generated by base editing for improvement of rice grain quality

“…The ACs of Indica (relatively high levels of more than 20%) and Japonica (intermediate levels of 14%–18%) rice are controlled by Wx a and Wx b alleles, respectively (Sano, 1984). The Wx op/hp , Wx mq , Wx la , Wx mp , and Wx mv alleles contributing to soft rice varieties with AC values commonly lower than <14%, have been successfully introgressed in modern rice breeding to generate cultivars with both good ECQ and/or grain transparency (Zhu et al,2015; Zhang et al, 2020; Zhou et al, 2020).…”

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

“…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 ). Not only being limited to these functional waxy alleles ( Wx ) these days, many researchers have been increasing their interests on other starch synthesis-related genes (SSRGs), like SSII / ALK (alkali degeneration) genes for the improvement of ECQ rice (Huang et al, 2020 , 2021 ).…”

“…Moreover, the origin of a new novel waxy allele Wx Ia (a combined mutation of Wx in and Wx b ) provided new insights of a unique phenotype into rice quality improvement (Zhou et al, 2021 ), and the other five old functional waxy alleles, namely, Wx b , Wx mp , Wx op , Wx in , and Wx a , identified in their sequencing analyses are distinguishable by their specific polymorphic sites in intron 1 and exons 2, 4, 6, and 10, respectively (Zhang et al, 2019 ). As an additional consequence, a new rare transgenic waxy allele “ Wx mw ” exhibited by a moderate GBSSI was also introduced, resulting in a moderate AC (Zhang et al, 2021 ). Therefore, it can be assumed that several functional waxy alleles have been characterized for their different major polymorphic sequences (Zhang et al, 2021 ).…”

“…As an additional consequence, a new rare transgenic waxy allele “ Wx mw ” exhibited by a moderate GBSSI was also introduced, resulting in a moderate AC (Zhang et al, 2021 ). Therefore, it can be assumed that several functional waxy alleles have been characterized for their different major polymorphic sequences (Zhang et al, 2021 ). For maize waxy alleles, many mutant alleles have been identified (more than 50 alleles) (Huang et al, 2010 ), and most were insertions or deletions (Huang et al, 2010 ; Xiaoyang et al, 2017 ), representing the most recent mutant allele by wx-Reina in Chinese waxy maize (Wu et al, 2019 ).…”

FLOURY ENDOSPERM19 encoding a class I glutamine amidotransferase affects grain quality in rice

“…The base substitutions in ALK cause amino acid changes in SSSII-3 and result in the alteration of enzymatic activity, and thereafter alter the ne structure of crystalline lamellae of amylopectin, and are nally re ected in GT (Gao et al 2011). So far, most of the researches on CEQ have focused on the abundant Wx allelic variations and ALK gene (Zhang et al 2019;Zhang et al 2020b;Hori et al 2021;Zhou et al 2020), or the interaction between them (Yang et al 2018a). Protein content is also an important factor affecting CEQ.…”