Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice

Abstract

Grain size and shape are important components determining rice grain yield, and they are controlled by quantitative trait loci (QTLs). Here, we report the cloning and functional characterization of a major grain length QTL, qGL3, which encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1). We found a rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The Kelch domains are essential for the OsPPKL1 biological function. Field trials showed that the application of the qgl3 allele could significantly increase grain yield in both inbred and hybrid rice varieties, due to its favorable effect on grain length, filling, and weight.QTL mapping | positional cloning | Oryza sativa L.

Natural Variations in SLG7 Regulate Grain Shape in Rice

“…GS3, encoding a transmembrane protein containing four putative domains, was the first characterized QTL that regulates grain length (Fan et al 2006). qGL3 encodes a putative protein phosphatase with a Kelch-like repeat domain, and an aspartate-to-glutamate transition in the second Kelch domain leads to a long-grain phenotype (Zhang et al 2012). GW6 encodes a GNAT-like protein that harbors intrinsic histone acetyltransferase activity, and an elevated expression enhances grain length and weight by enlarging spikelet hulls and accelerating grain filling (Song et al 2015).…”

Haplotypes of qGL3 and their roles in grain size regulation with GS3 alleles in rice

“…Zhang et al (2012) found that only SNP1 in the qGL3 region in 94 germplasms (the same SNP that was found in TD70) contributed highly to grain length, whereas other polymorphic sites had no significant contributions to grain length. According to the coding sequence, GS3 has at least four different alleles (Mao et al, 2010).…”

“…Although the location of qGL3 and GS3 genes on chromosome 3 was close, they did not exhibit genetic linkage characteristics (Fan et al, 2006;Zhang et al, 2012). We found that qGL3 can not only be freely combined and separated in the offspring, but it can also be stably integrated with GS3 in the same varieties.…”

“…Grain shape, as the major determinant of grain weight, is characterized by a combination of four parameters: grain length, grain width, grain thickness, and filling degree (Xing and Zhang, 2010;Huang et al, 2013;Ikeda et al, 2013;Zuo and Li, 2014). In recent years, several key genes that regulate grain shape were identified (Fan et al, 2006;Shomura et al, 2008;Weng et al, 2008;Li et al, 2011;Zhang et al, 2012;Ishimaru et al, 2013;Song et al, 2007Song et al, , 2015Wang et al, 2012Wang et al, , 2015a. For instance, qGL3/qGL3.1 is a newly identified QTL associated with grain length, which exhibited the highest logarithm of the odds value and the greatest phenotypic variation compared to other markers, and it also significantly contributed to grain thickness and grain width (Hu et al, 2012;Qi et al, 2012;Zhang et al, 2012).…”

“…In recent years, several key genes that regulate grain shape were identified (Fan et al, 2006;Shomura et al, 2008;Weng et al, 2008;Li et al, 2011;Zhang et al, 2012;Ishimaru et al, 2013;Song et al, 2007Song et al, , 2015Wang et al, 2012Wang et al, , 2015a. For instance, qGL3/qGL3.1 is a newly identified QTL associated with grain length, which exhibited the highest logarithm of the odds value and the greatest phenotypic variation compared to other markers, and it also significantly contributed to grain thickness and grain width (Hu et al, 2012;Qi et al, 2012;Zhang et al, 2012). A comparison of functional and nonfunctional sequences revealed a single nucleotide substitution (C→A) at position 1092 in exon 10, resulting in the replacement of Asp (D) (a non-functional allele) with Glu (E) (a functional allele) at the 364th amino acid.…”