Effect of multiple allelic combinations of genes on regulating grain size in rice

Ngangkham, Umakanta; Samantaray, Sanghamitra; Yadav, Manoj Kumar; Kumar, Awadhesh; Parameswaran, C.; Katara, Jawahar Lal

doi:10.1371/journal.pone.0190684

Cited by 33 publications

(31 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A correlation analysis between GL and GW showed a highly significant ( p ≤ 0.01) but negative association (r = −0.604 **) between these two traits. Such a negative linear relationship has also been reported by other researchers [20,55]. GL and GT were also negatively correlated (r = −0.398 *), which was also significant ( p ≤ 0.05) and strong.…”

Section: Resultssupporting

confidence: 86%

“…A number of genes and their alleles in different combinations have been found to be involved in determining the ultimate size, shape, and weight of rice grains (also detected by previous researchers) [7,8,9,10,11,12,13,14,15,16,17,18,19,20]. An amplification profile of 14 Insertion/Deletion (InDel) markers of nine studied genes related to grain size and weight in 204 rice germplasms is given in Figure 5.…”

Section: Resultsmentioning

confidence: 63%

“…InDel polymorphisms are the second most abundant (after SNPs) forms of genetic variations in animals and plants, with great diversity. Moreover, previous studies only showed the contributions of the reported genes in regulating these grain traits separately [11,15,16,19,20,59,60]. However, recent studies have shown the modes of InDel based allelic contributions in the expression of grain size, as well as weight related traits, the allelic combination of all the InDel marker loci involved in the final texture of the rice grains, and the potential of each loci in regulating these traits in rice.…”

Section: Discussionmentioning

confidence: 99%

“…A number of Quantitative Trait Loci (QTLs) for grain appearance and weight have already been investigated and reported by different scientists [7,8,9,10,11,12,13,14,15,16,17,18,19,20]. More often, grain length, thickness, and width are regarded as determinants of grain appearance whereas the 1000 grain weight determines grain weight and eventually grain yield.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice (Oryza sativa L.)

Gull

Haider²,

et al. 2019

IJMS

View full text Add to dashboard Cite

The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major genes, qPE9~1, GW2, SLG7, GW5, GS3, GS7, GW8, GS5, and GS2, in regulating four size and weight related traits, i.e., grain length (GL), grain width (GW), grain thickness (GT), and thousand grain weight (TGW) in 204 diverse rice germplasms using Insertion/Deletion (InDel) markers. The studied germplasm displayed wide-ranging variability in the four studied traits. Except for three genes, all six genes showed considerable association with these traits with varying strengths. Whole germplasm of 204 genotypes could be categorized into three major clusters with different grain sizes and weights that could be utilized in rice breeding programs where grain appearance and weight are under consideration. The study revealed that TGW was 24.9% influenced by GL, 37.4% influenced by GW, and 49.1% influenced by GT. Hence, assuming the trend of trait selection, i.e., GT > GW > GL, for improving TGW in the rice yield enhancement programs. The InDel markers successfully identified a total of 38 alleles, out of which 27 alleles were major and were found in more than 20 genotypes. GL was associated with four genes (GS3, GS7, GW8, and GS2). GT was also found to be regulated by four different genes (GS3, GS7, GW8, and GS2) out of the nine studied genes. GW was found to be under the control of three studied genes (GW5, GW8, and GS2), whereas TGW was found to be under the influence of four genes (SLG7, GW5, GW8, and GS5) in the germplasm under study. The Unweighted Pair Group Method with Arithmetic means (UPGMA) tree based on the studied InDel marker loci segregated the whole germplasm into three distinct clusters with dissimilar grain sizes and weights. A two-dimensional scatter plot constructed using Principal Coordinate Analysis (PCoA) based on InDel markers further separated the 204 rice germplasms into four sub-populations with prominent demarcations of extra-long, long, medium, and short grain type germplasms that can be utilized in breeding programs accordingly. The present study could help rice breeders to select a suitable InDel marker and in formulation of breeding strategies for improving grain appearance, as well as weight, to develop rice varieties to compete international market demands with higher yield returns. This study also confirms the efficient application of InDel markers in studying diverse types of rice germplasm, allelic frequencies, multiple-gene allele contributions, marker-trait associations, and genetic variations that can be explored further.

show abstract

Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice (Oryza sativa L.)

Gull

Haider²,

et al. 2019

IJMS

View full text Add to dashboard Cite

show abstract

“…GW5 / qSW5 and HGW genes identified by map-based cloning encode a polyubiquitin-interacting nuclear protein and a novel plant-specific ubiquitin domain protein, respectively [ 20 , 31 ], which strongly suggests that GW5/qSW5, HGW, and GW2 function in the same ubiquitination pathway for the regulation of rice grain size and weight, although they may function with different target proteins. Very recently, six genes DEP1 , GS7 , GS3 , GW8 , GL7 , and GS , but not GW2 , were reported to be strongly associated with grain size traits [ 32 ], suggesting that GW2 acts in a different pathway from these genes.…”

Section: Discussionmentioning

confidence: 99%

GW2 Functions as an E3 Ubiquitin Ligase for Rice Expansin-Like 1

Choi

Kim

Markkandan

et al. 2018

IJMS

View full text Add to dashboard Cite

Seed size is one of the most important traits determining the yield of cereal crops. Many studies have been performed to uncover the mechanism of seed development. However, much remains to be understood, especially at the molecular level, although several genes involved in seed size have been identified. Here, we show that rice Grain Width 2 (GW2), a RING-type E3 ubiquitin ligase, can control seed development by catalyzing the ubiquitination of expansin-like 1 (EXPLA1), a cell wall-loosening protein that increases cell growth. Microscopic examination revealed that a GW2 mutant had a chalky endosperm due to the presence of loosely packed, spherical starch granules, although the grain shape was normal. Yeast two-hybrid and in vitro pull-down assays showed a strong interaction between GW2 and EXPLA1. In vitro ubiquitination analysis demonstrated that EXPLA1 was ubiquitinated by GW2 at lysine 279 (K279). GW2 and EXPLA1 colocalized to the nucleus when expressed simultaneously. These results suggest that GW2 negatively regulates seed size by targeting EXPLA1 for degradation through its E3 ubiquitin ligase activity.

show abstract

Aromatic rice (Oryza sativa L.) landraces of Indo‐Gangetic Plains of India harbor rich genetic diversity

Bairwa,

Yadav,

Tiwari

et al. 2024

Crop Science

View full text Add to dashboard Cite

Aromatic rice (Oryza sativa L.) germplasm conserved in global genebanks needs intensive characterization to assess genetic diversity and population structure for crop improvement. We analyzed a panel of 92 accessions of non‐Basmati aromatic rice landrace germplasm with 23 phenotypic traits and 48 microsatellite markers. The landrace accessions displayed a huge phenotypic diversity for traits, namely, culm length, flag‐leaf length, panicle‐bearing tillers (PBT), plant height, panicle length, peduncle length, panicle exsertion, grain length, grain width, hull color, and 1000‐grain weight (TGW). Phenotypic clustering revealed three major clusters and five principal components explained 81.24% of the variance. TGW was associated positively with grain length, grain width, peduncle length, and grain yield but negatively with culm length and PBT. A total of 528 microsatellite alleles were detected, with 11.0 alleles per locus, revealing the presence of high polymorphism. Genetically, four subpopulations were detected based on structure analysis. In the germplasm, high levels of gene flow (Nm = 1.51) and gene diversity (HE = 0.83) were found. Among the subpopulations, we discovered high levels of inbreeding (FIS = 0.92) and moderate genetic differentiation (FST = 0.14). High polymorphism information content (0.806) along with a high level of molecular variance among genotypes (79%) was detected. A large number of multiple alleles were detected in numerous landrace accessions, revealing the presence of heterogeneity and heterozygotes in the landrace germplasm. The results of the present study are vital for the utilization of landrace diversity in the genetic improvement programs designed for rice quality improvement and consumer preference.

show abstract

Effect of multiple allelic combinations of genes on regulating grain size in rice

Cited by 33 publications

References 47 publications

InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice (Oryza sativa L.)

InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice (Oryza sativa L.)

GW2 Functions as an E3 Ubiquitin Ligase for Rice Expansin-Like 1

Aromatic rice (Oryza sativa L.) landraces of Indo‐Gangetic Plains of India harbor rich genetic diversity

Contact Info

Product

Resources

About