qTGW12a, a naturally varying QTL, regulates grain weight in rice

Abstract

Key message A stable QTL associated with rice grain type with a large effect value was found in multiple environments, and its candidate genes were verified by genetic transformation. Abstract Rice (Oryza sativa L.) grain size is critical to both yield and appearance quality. Therefore, the discovery and identification of rice grain size genes can provide pathways for the cultivation of high-yielding varieties. In the present work, 45,607 SNP markers were used to construct a high-density genetic map of rice recombinant inbred lines, and hence a total of 14 quantitative trait loci (QTLs) were detected based on the phenotypic data of grain weight, grain length and grain width under four different environments. qTGW12a and qGL12 are newly detected QTLs related to grain weight, and are located between 22.43 Mb and 22.45 Mb on chromosome 12. Gene annotation shows that the QTL region contains the LOC_Os12g36660 annotated gene, which encodes the multidrug and toxic compound extrusion (MATE) transporter. Mutations in exons and the splice site were responsible for the changes in grain type and weight. Gene knockout experiments were used to verify these results. Hence, these results provide a basis for the cloning of qTGW12a. This discovery provides new insights for studying the genetic mechanism of rice grain morphology, and reveals a promising gene to ultimately increase rice yield.

Non-vernalization requirement in Chinese kale caused by loss of BoFLC and low expressions of its paralogs

“…In contrast, bulked segregant analysis is a fast, economical, and efficient method for genetic analysis (Michelmore et al 1991 ). High-throughput sequencing technology is now frequently used in combination with BSA to study complex genetic traits such as leaf colors and heading traits in lettuce (Su et al 2020 ; Yu et al 2020 ), fruit shape trait in wax gourd (Cheng et al 2021 ), blossom-end rot trait in tomato (Topcu et al 2021 ), grain weight in rice (Du et al 2021 ), fruit spines in spinach (Liu et al 2021 ). In this study, we employed BSA + RNA-seq method to identify the candidate gene BoFLC, which further confirmed that BSA + high-throughput sequencing could greatly facilitate the cloning of genes controlling complex genetic traits.…”

SLG2 specifically regulates grain width through WOX11‐mediated cell expansion control in rice

“…Of the 17 cell expansion genes that appear to express in young panicles ( https://ricexpro.dna.affrc.go.jp/GGEP/ ), six genes ( OsEXPA1 , OsEXPA4 , OsEXPA5 , OsEXPA26 , OsEXPB7 and OsEXPB13 ) showed suppressed transcription in slg2 relative to WT (Figure 1m ). We also explored the possible regulatory relationship between SLG2 and previously identified grain width‐related genes by detecting the expression level of these genes, including GW2 (Song et al ., 2007 ), GS5 (Li et al ., 2011 ), GS6 (Sun et al ., 2013 ), GW8 (Wang et al ., 2012 ), GW5 (Liu et al ., 2017 ), GW5L (Tian et al ., 2019 ), TGW2 (Ruan et al ., 2020 ), GW6 (Shi et al ., 2020 ) and TGW12a (Du et al ., 2021 ). We did not find significant differences in the transcripts abundance of these genes between slg2 and WT (Figure S3b ).…”

“…By studying germplasms with different grain shapes, about 22 quantitative trait loci (QTLs) have been identified to regulate grain size in rice (Jiang et al ., 2022 ). However, a careful survey of the phenotypes of the loss of function mutants, but not near isogenic lines or knockdown/overexpression transgenic lines, revealed that most of these genes show influence on the development of grains in multi‐dimensions, and only four genes GS5 (Li et al ., 2011 ), GW5 (Tian et al ., 2019 ), TGW2 (Ruan et al ., 2020 ) and TGW12a (Du et al ., 2021 ) display a regulatory role confined to grain width. However, the application value of these four genes in regulating grain width remains to be evaluated, as they all seem to affect the grain filling process.…”

Dissection of Closely Linked Quantitative Trait Locis Controlling Grain Size in Rice

“…Remarkable progress has been achieved by the discovery of large-effect QTLs affecting the yield and quality in recent years. Notably, rarely have small-effect QTLs been cloned in rice ( Chan et al, 2020 ; Du et al, 2021 ). It is recognized that the complex traits, especially as grain yield and its component traits, were controlled by many genes.…”

“…Notably, qTGW1.2b regulates grain weight which encodes a VQ-motif protein OsVQ4 ( Chan et al, 2020 ). A naturally varying QTL, the qTGW12a , which encodes the multidrug and the toxic compound extrusion (MATE) transporter, regulates grain weight in rice ( Du et al, 2021 ). Validation and dissection of more small-effect QTLs could provide a large number of the candidate genes and would be beneficial for establishing the network-controlling grain weight and grain size in rice.…”