Fine mapping and identification of a novel locus qGL12.2 control grain length in wild rice (Oryza rufipogon Griff.)

Abstract

A wild rice QTL qGL12.2 for grain length was fine mapped to an 82-kb interval in chromosome 12 containing six candidate genes and none was reported previously. Grain length is an important trait for yield and commercial value in rice. Wild rice seeds have a very slender shape and have many desirable genes that have been lost in cultivated rice during domestication. In this study, we identified a quantitative trait locus, qGL12.2, which controls grain length in wild rice. First, a wild rice chromosome segment substitution line, CSSL41, was selected that has longer glume and grains than does the Oryza sativa indica cultivar, 9311. Next, an F population was constructed from a cross between CSSL41 and 9311. Using the next-generation sequencing combined with bulked-segregant analysis and F recombinants analysis, qGL12.2 was finally fine mapped to an 82-kb interval in chromosome 12. Six candidate genes were found, and no reported grain length genes were found in this interval. Using scanning electron microscopy, we found that CSSL41 cells are significantly longer than those of 9311, but there is no difference in cell widths. These data suggest that qGL12.2 is a novel gene that controls grain cell length in wild rice. Our study provides a new genetic resource for rice breeding and a starting point for functional characterization of the wild rice GL gene.

Fine mapping qGL2H, a major locus controlling grain length in barley (Hordeum vulgare L.)

“…A promising candidate for the control of grain length is HORVU2Hr1G089310 which encodes a MYB transcription factor protein of subgroup 15. Previous research in other cereal species has indicated that transcription factors are heavily involved in the control of grain size through regulation of cell proliferation and differentiation (Arora et al 2017;Gong et al 2018;Ji et al 2019;Qi et al 2018). Specifically, a MYB transcription factor designated GL4 was shown to regulate cell elongation in the outer and inner glumes of African rice which directly regulated grain length (Wu et al 2017).…”

“…We identified one promising candidate gene that based on current research is likely to regulate grain size, annotated as HORVU2Hr1G089310 and encoding a MYB transcription factor. MYB-like proteins represent one of the largest families of transcription factors and have been linked to numerous biological functions, including abiotic stress tolerance and control of grain size characteristics through regulation of cell division and differentiation within certain developmental tissues (Qi et al 2018;Wu et al 2017;Xiong et al 2014). While the other two candidate genes cannot be ruled out, the MYB transcription factor represents the most promising avenue on which to focus further research.…”

“…Within this newly mapped interval, three highconfidence predicted genes were identified, HOR-VU2Hr1G089310, a predicted MYB transcription factor of subgroup 15, which is a promising candidate as it has been reported to be involved in cell cycle control and cell division in the longitudinal direction (Qi et al 2018;Tombuloglu et al 2013;Wu et al 2017). The other predicted genes were HORVU2Hr1G089320 (hexosyltransferase) and HORVU2Hr1G089330 (root UV-B sensitive 2 protein).…”

Identification and genetic analysis of qCL1.2 , a novel allele of the “green revolution” gene SD1 from wild rice ( Oryza rufipogon ) that enhances plant height

“…CSSLs are an excellent platform for studying wild alleles in cultivated rice genetic backgrounds. In our laboratory, a set of CSSLs of wild rice was constructed and used for gene discovery, resulting in the discovery of many QTLs related to important agronomic traits [10,17]. In the current study, a main PH QTL, qCL1.2, was identi ed.…”

“…In our previous study, a set of CSSLs was constructed with wild rice as the donor parent and the indica cultivar 9311 as the recurrent parent. Many quantitative trait loci (QTLs) correlated with important agronomic traits have been identi ed using the CSSL platform [16][17][18]. In this study, we ne mapped a novel allele of the "green revolution" gene sd1 using a CSSL population.…”