Genetic Dissection of Grain Size Traits Through Genome-Wide Association Study Based on Genic Markers in Rice

Nayak, Amrit Kumar; Kumar, C. T. A.; Behera, Sasmita; Sah, Rameswar Prasad; Lavanya, G. Roopa; Kumar, Awadhesh; Behera, Lambodar; Azharudheen, T. P. Muhammed

doi:10.1016/j.rsci.2022.07.006

Cited by 15 publications

(12 citation statements)

References 59 publications

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“…The correlation analysis among characters showed that there was a positive correlation between TGW and GL, GW, and GT in the indica group as the main cultivation type of the Hani terraces. However, there was no significant correlation between LWR and TGW in the indica or japonica group, which was consistent with previous research results [33][34][35][36]. An increase in GL, GW, and GT contributed to an increase in grain weight, with little contribution from LWR.…”

Section: Phenotypic Evaluationsupporting

confidence: 88%

Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province

Lei

Wang

et al. 2023

Plants

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The Honghe Hani Rice Terraces System (HHRTS) of Yunnan Province is an important agricultural and cultural heritage landscape. Until now, a large number of local rice landraces have been planted. Mining excellent genes contained in these landraces provides a reference for variety improvement and new variety breeding. In this study, 96 rice landraces collected from the Hani terraces were planted in Honghe Mengzi, Yunnan Province, in 2013, 2014, 2015, and 2021, and five major grain traits were measured and analyzed. The genomic variation of 96 rice landraces was scanned by 201 simple sequence repeat (SSR) markers. The genetic diversity, population structure, and genetic relationships of the natural population were analyzed. The mixed linear model (MLM) method of the TASSEL software was used to analyze the associations between markers and traits. A total of 936 alleles were amplified by 201 pairs of SSR primers. The average number of observed alleles (Na), the effective number of alleles (Ne), Shannon’s information index (I), heterozygosity (H), and the polymorphism information content (PIC) per marker were 4.66, 2.71, 1.08, 0.15, and 0.55, respectively. Ninety-six landraces were divided into two groups by population structure, clustering, and principal component analysis, and indica rice was the main group. The coefficients of variation of the five traits ranged from 6.80 to 15.24%, and their broad heritabilities were more than 70%. In addition, there were positive correlations among the same grain traits between different years. Through MLM analysis, 2, 36, 7, 7, and 4 SSR markers were significantly associated with grain length (GL), grain width (GW), grain thickness (GT), grain length–width ratio (LWR), and thousand-grain weight (TGW), respectively. The explanation rates of phenotypic variation were 16.31 (RM449, Chr. 1)—23.51% (RM316, Chr. 9), 10.84 (RM523, Chr. 3; RM161/RM305, Chr. 5)—43.01% (RM5496, Chr. 1), 11.98 (RM161/RM305, Chr. 5)—24.72% (RM275, Chr. 6), 12.68 (RM126, Chr. 8)—36.96% (RM5496, Chr. 1), and 17.65 (RM4499, Chr. 2)—26.32% (RM25, Chr. 8), respectively. The associated markers were distributed on 12 chromosomes of the genome.

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Section: Phenotypic Evaluationsupporting

confidence: 88%

Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province

Lei

Wang

et al. 2023

Plants

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“…The Quechi variety expressed the best results for number of grains per panicle. The number of grains per panicle per plant is the most significant component in rice yield (Nayak et al, 2022). The qualitative descriptors were also assessed to show the dissimilarity level present in the different varieties (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

“…Rice (Oryza sativa L.) is the basic food for billions of people and is considered one of the most important food crops in the world (Niqing He et al, 2022). However, economic and political globalization, together with the generalized adoption of high yield commercial varieties has led to a significant loss of genetic diversity in rice and landrace rice varieties have been abandoned (Lei et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Morphoagronomic descriptors of rice landraces varieties (Oryza sativa L.) from the state of Maranhão

Moreira,

Oliveira,

Silva

et al. 2024

Cad. Pedagógico

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Rice landrace varieties are adapted to the most diverse environmental conditions, which is clearly important in periods of great climatic and sanitary uncertainties. However, there is a gap in their description in the literature. Maranhão, Brazil, has wide diversity in landrace seeds, with rice varieties that can significantly contribute to the genetic breeding of the species. Based on this information, the objective of the present study was to characterize the landraces rice varieties, through the description of the morphological and agronomic profile. The study analyzed 23 qualitative heredity descriptors and three quantitative descriptors in 21 rice landrace varieties from different locations in the state of Maranhão, according to the methodological procedures recommended by the National Cultivar Protection Service. A randomized block e experimental design was used (DBC), with 21 treatments and four replications. Considering complementing To complement the study, a multicategorical analysis was carried out between the 21 accessions, based on qualitative data obtained from the 22 morphological descriptors, which generated a dendrogram. The results showed that there are differences between the qualitative descriptors. Quantitative descriptors are highly significant, with regard to the number of tillers, with emphasis on the Edinho variety. The Quechi variety was responsible for one of the factors that most influences the rice yield, with the highest number of grains per panicle. The varieties Codozinho, Edinho, Palha Murcha and Pé Roxo, are more productive in number of panicles. The dendrogram formed three clusters with evidence of dissimilarities between the varieties. The results show that the landrace varieties differ in their morphoagronomic characteristics and can be valuable materials in the construction of a new, more sustainable agriculture.

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“…It is crucial to have control over population structure in GWAS to prevent spurious marker–trait associations ( Nayak et al., 2022 ). The origin, selection pressure, and reproductive behavior of genotypes all have an impact on familial relatedness among individuals in an association panel ( Atwell et al., 2010 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association studies for a comprehensive understanding of the genetic architecture of culm strength and yield traits in rice

Badri,

Padmashree,

Anilkumar

et al. 2024

Front. Plant Sci.

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Lodging resistance in rice is a complex trait determined by culm morphological and culm physical strength traits, and these traits are a major determinant of yield. We made a detailed analysis of various component traits with the aim of deriving optimized parameters for measuring culm strength. Genotyping by sequencing (GBS)-based genome-wide association study (GWAS) was employed among 181 genotypes for dissecting the genetic control of culm strength traits. The VanRaden kinship algorithm using 6,822 filtered single-nucleotide polymorphisms (SNPs) revealed the presence of two sub-groups within the association panel with kinship values concentrated at<0.5 level, indicating greater diversity among the genotypes. A wide range of phenotypic variation and high heritability for culm strength and yield traits were observed over two seasons, as reflected in best linear unbiased prediction (BLUP) estimates. The multi-locus model for GWAS resulted in the identification of 15 highly significant associations (p< 0.0001) for culm strength traits. Two novel major effect marker–trait associations (MTAs) for section modulus and bending stress were identified on chromosomes 2 and 12 with a phenotypic variance of 21.87% and 10.14%, respectively. Other MTAs were also noted in the vicinity of previously reported putative candidate genes for lodging resistance, providing an opportunity for further research on the biochemical basis of culm strength. The quantitative trait locus (QTL) hotspot identified on chromosome 12 with the synergistic association for culm strength trait (section modulus, bending stress, and internode breaking weight) and grain number can be considered a novel genomic region that can serve a dual purpose of enhancing culm strength and grain yield. Elite donors in the indica background with beneficial alleles of the identified major QTLs could be a valuable resource with greater significance in practical plant breeding programs focusing on improving lodging resistance in rice.

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Genetic Dissection of Grain Size Traits Through Genome-Wide Association Study Based on Genic Markers in Rice

Cited by 15 publications

References 59 publications

Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province

Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province

Morphoagronomic descriptors of rice landraces varieties (Oryza sativa L.) from the state of Maranhão

Genome-wide association studies for a comprehensive understanding of the genetic architecture of culm strength and yield traits in rice

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