GLW7.1, a Strong Functional Allele of Ghd7, Enhances Grain Size in Rice

Abstract

Grain size is a key determinant of both grain weight and grain quality. Here, we report the map-based cloning of a novel quantitative trait locus (QTL), GLW7.1 (Grain Length, Width and Weight 7.1), which encodes the CCT motif family protein, GHD7. The QTL is located in a 53 kb deletion fragment in the cultivar Jin23B, compared with the cultivar CR071. Scanning electron microscopy analysis and expression analysis revealed that GLW7.1 promotes the transcription of several cell division and expansion genes, further resulting in a larger cell size and increased cell number, and finally enhancing the grain size as well as grain weight. GLW7.1 could also increase endogenous GA content by up-regulating the expression of GA biosynthesis genes. Yeast two-hybrid assays and split firefly luciferase complementation assays revealed the interactions of GHD7 with seven grain-size-related proteins and the rice DELLA protein SLR1. Haplotype analysis and transcription activation assay revealed the effect of six amino acid substitutions on GHD7 activation activity. Additionally, the NIL with GLW7.1 showed reduced chalkiness and improved cooking and eating quality. These findings provide a new insight into the role of Ghd7 and confirm the great potential of the GLW7.1 allele in simultaneously improving grain yield and quality.

geneHapR: an R package for gene haplotypic statistics and visualization

“…In this step, accessions with heterozygotes or missing genotypes were eliminated. Finally, in line with previous studies [ 21 ], a total of 499 accessions and 8 main haplotypes were remained after elimination of rare haplotypes and missing genotypes.…”

“…For demonstrating the usage of geneHapR, the genotype and phenotype data and annotation of a grain size regulating gene OsGHD7 [ 20 , 21 ] were retrieved from Rice Variation Map [ 22 ] and Rice Functional Genomics and Breeding [ 23 ] and Rice Genome Annotation Project [ 24 ], respectively. The R script used for haplotype identification and visualzation of OsGHD7 could be found in additional file 1 .…”

Fine Mapping of Five Grain Size QTLs Which Affect Grain Yield and Quality in Rice

“…Moreover, the differential expression of cell expansion-related genes, such as EXPA5, EXPA10, EXPA6 and EXPA7; EXPA3, EXPA10, and EXPB7; EXPA10; and EXPA6 and EXPB7, were observed within the regulatory modules of qGW1-qGW7, qGW5-qGW7, qGW1-qGW5-qGW7, qGW1-qGW7-qGW12, and qGW5-qGW7-qGW12, respectively (Figure 9A,B), suggesting qGW1-qGW7-qGW12 influences cell size and grain width by altering the expression of EXPA6. Numerous QTLs and genes have been reported to regulate grain size by influencing the expression of cell division and expansion-related genes, such as qTGW2b [88], GLW7.1 [89], GL3.1 [38], and GS2 [90]. In addition, negative correlations were observed between gene expression and grain yield for both qGW1 and qGW7.…”

“…Notably, positive correlations were observed between gene expression and grain yield for both qGL9 and qGW12. Variations in the expression of genes associated with cell division and expansion not only impact grain size, but also influence grain yield [38,89,90].…”

“…The combination of the OsMADS1 lgy3 allele with dep1-1 and gs3 alleles has the potential to simultaneously improve both grain yield and quality in rice [14]. GLW7.1 also represents a novel way to breed high-yield and superior-quality varieties [89].…”