Identification and Pleiotropic Effect Analysis of GSE5 on Rice Chalkiness and Grain Shape

Abstract

Chalkiness is one of several major restricting factors for the improvement of rice quality. Although many chalkiness-related quantitative trait loci have been mapped, only a small number of genes have been cloned to date. In this study, the candidate gene GSE5 of a major quantitative trait locus (QTL) for rice chalkiness, qDEC5, was identified by map-based cloning. Phenotyping and haplotype analysis of proActin:GSE5 transgenic line, gse5-cr mutant, and 69 rice varieties further confirmed that GSE5 had the pleiotropic effects and regulated both chalkiness and grain shape. Genetic analysis showed GSE5 was a dominant gene for grain length and a semi-dominant gene for grain width and chalkiness. The DNA interval closely linked to GSE5 was introgressed to Zhenshan 97B (ZB) based on molecular marker-assisted selection, and the improved ZB showed lower chalkiness and longer but smaller grains, which showed that GSE5 played an important role in breeding rice varieties with high yield and good quality. Transcriptomics, proteomics, and qRT-PCR analyses showed that thirty-nine genes associated with carbon and protein metabolism are regulated by GSE5 to affect the formation of chalkiness, including some newly discovered genes, such as OsCESA9, OsHSP70, OsTPS8, OsPFK04, OsSTA1, OsERdj3A, etc. The low-chalkiness lines showed higher amino sugar and nucleotide sugar metabolism at 10 days after pollination (DAP), lower carbohydrate metabolism at 15 DAP, and lower protein metabolism at 10 and 15 DAP. With heat shock at 34/30°C, rice chalkiness increased significantly; OsDjC10 and OsSUS3 were upregulated at 6 and 12 DAP, respectively, and OsGSTL2 was downregulated at 12 DAP. Our results identified the function and pleiotropic effects of qDEC5 dissected its genetic characteristics and the expression profiles of the genes affecting the chalkiness formation, and provided a theoretical basis and application value to harmoniously pursue high yield and good quality in rice production.

Genetic Improvements in Rice Grain Quality: A Review of Elite Genes and Their Applications in Molecular Breeding

“…The correlation between grain shape and chalkiness has been confirmed, with certain QTLs such as gw2 [27] and GS2 [62] showing a significant increase in chalkiness while enhancing grain width/weight, and others such as GL7/GW7 [36,37], gw8 [35], and gs9 [39] reducing chalkiness percentage by increasing grain length and decreasing grain width. A recent study identified that the grain width QTL GW5/GSE5 has pleiotropic effects on both chalkiness and grain shape [47]. Introducing the GSE5 ZJB allele to the Indica rice varieties Zhenshan 97B showed lower chalkiness and longer but smaller grains.…”

Caracterización Morfológica Del Grano De La Variedad De Arroz Soberana Fl

“…De acuerdo con estos autores, este gen controla el ancho del grano a través de un proceso que restringe la proliferación de células en el casco de la espiguilla; no obstante, en la región promotora del gen GSE5 se presentan deleciones que son específicas para las sub-especies índicas y japónicas, las cuales restringen la expresión del gen y por ende reducen el tamaño del grano de las CARACTERIZACIÓN MORFOLÓGICA DEL GRANO Hatun Yachay Wasi 2(2), 2023 ISSN: 2955 -8255 variedades. Otros estudios han encontrado efectos pleiotrópicos del gen GSE5 sobre otros caracteres vinculados con la calidad del grano, tales como la longitud, forma y opacidad (centro blanco) del grano (Jiang et al, 2022). Estos estudios son de gran importancia en el cultivo, porque permiten conocer los efectos y perfiles de expresión de este gen, proveyendo las bases teóricas para la producción de cultivares que además de presentar elevados índices de productividad, también presenten una excelente calidad del grano.…”

Fine Mapping of Two Major Quantitative Trait Loci for Rice Chalkiness With High Temperature-Enhanced Additive Effects

“…The alleles GW7 , gw8 and gs9 caused much slenderer grain shape, resulting in the reducing of rice chalkiness ( Wang et al, 2012 , 2015 ; Zhao et al, 2018 ). Recently, Jiang et al (2021) identified GSE5 had a pleiotropic function to regulating grain shape and chalkiness by map-based cloning. Several genes for endosperm development have been found to influence grain-filling and chalkiness.…”