TGW3, a Major QTL that Negatively Modulates Grain Length and Weight in Rice

Abstract

Grain length (size) and weight are essential components of crop yield. To date, many QTLs/genes for these traits have been identified. GS3 encodes a putative transmembrane protein and functions as a negative regulator, and its larger-grain allele contains a nonsense mutation causing a 178-aa truncation (Fan et al., 2006). GL3.1/qGL3 encodes a putative protein phosphatase and also acts as a negative regulator of grain size (Qi et al., 2012;Zhang et al., 2012). Another negative regulator of grain size and weight is TGW6, which hydrolyzes indole-3-acetic acid (IAA)-glucose into IAA and glucose (Ishimaru et al., 2013). In contrast, GW6a is a positive regulator of grain weight, which encodes a novel histone H4 acetyltransferase (Song et al., 2015). Copy number variation at the GL7/GW7 locus causes elevated expression of GL7 and thus an increase in grain length (Wang et al., 2015a(Wang et al., , 2015b. GL2/GS2 encodes the plant-specific transcription factor OsGRF4, and its larger-grain allele harbors a mutation preventing cleavage by miR396c, resulting in elevated GL2/GS2 expression (Hu et al., 2015;Che et al., 2016). GLW7 encodes the plantspecific transcription factor OsSPL13, and high OsSPL13 expression is associated with larger grains (Si et al., 2016). These findings have greatly enhanced our understanding of grain length and weight regulation; however, there are still gaps in integrating these factors into genetic network(s). Here, we report a thorough dissection of the QTL composition of grain size and the characterization of a novel QTL, qTGW3, that regulates grain length and weight in rice.

Genome-Wide Association Study of Grain Size Traits in Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Population

“…Recent advances in rice functional genomics facilitated the cloning and functional characterization of several genes that either positively or negatively regulates grain size. Negative grain size regulators that were previously cloned include GS3 (Fan et al, 2006), GW2 (Song et al, 2007), TGW6 (Ishimaru et al, 2013), GW7/GL7/SLG7 (Wang et al, 2015a,c;Zhou et al, 2015), qGL3/qTGW3 (Ying et al, 2018), and LARGE8 (Xu et al, 2018); whereas positive grain size regulators include GW5/qSW5 (Shomura et al, 2008;Weng et al, 2008), GS5 (Li et al, 2011), GW8/OsSPL16 (Wang et al, 2012b), GS2 (Duan et al, 2015;Hu et al, 2015), BG1 (Liu et al, 2015), WTG1 (Huang et al, 2017;Liu et al, 2018), GS9 (Zhao et al, 2018), and qLGY3/OsLG3b (Yu et al, 2018). It is noteworthy that these cloned genes control grain size by altering cell proliferation and/or cell expansion affecting cell numbers either in latitudinal or longitudinal directions.…”

Genome-Wide Identification of QTLs for Grain Protein Content Based on Genotyping-by-Resequencing and Verification of qGPC1-1 in Rice

“…The HHZ/JZ1560 mapping population consisting of 280 RILs was developed using the single-seed descendent method by Ying et al [29]. HHZ is an indica variety as the female parent with small grains and being widely cultivated in China, while JZ1560 is a japonica rice accession with very large grains ( Figure S2).…”

“…The high-density linkage map constructed by one of the GBR method, specific length amplified fragment, was composed of 18,194 SNP markers and spanned 2132.56 cM with an average genetic distance of 0.12 cM. In our previous study, we constructed the SLAF library for each RIL and the products were further sequenced using Illumina HiSeq 2500 system (Illumina, Inc.; San Diego, CA, USA) [29]. Polymorphism loci between the parents were identified for the selection of high-quality SNP markers after filtering out the low-quality raw reads.…”

Peer Review #2 of "Fine-mapping of qTGW2, a quantitative trait locus for grain weight in rice (Oryza sativa L.) (v0.2)"

“…So far, 16 QTLs for these traits with large effects were cloned using diverse mapping populations. Among these, ten genes regulate grain weight by mainly affected grain length, including GS2/ GL2, OsLG3, OsLG3b, GS3, GL3.1/qGL3, qTGW3/ TGW3/GL3.3, TGW6, GW6a, GL6, and GLW7 (Fan et al, 2006;Qi et al, 2012;Zhang et al, 2012;Ishimaru et al, 2013;Hu et al, 2015;Song et al, 2015;Che et al, 2016;Si et al 2016;Yu et al, 2017;Hu et al, 2018;Xia et al, 2018;Ying et al, 2018;Yu et al, 2018;. Other four genes regulate grain weight by primarily influencing grain width, including GW2, GS5, GSE5 and GW8 (Song et al, 2007;Li et al, 2011;Wang et al, 2012;Duan et al, 2017).…”