Development of SNP Markers from GWAS for Selecting Seed Coat and Aleurone Layers in Brown Rice (Oryza sativa L.)

Kim, Me-Sun; Ko, Seo-Rin; Le, Van Trang; Jee, Moo-Gun; Jung, Yu Jin; Kang, Kwon-Kyoo; Cho, Yong-Gu

doi:10.3390/genes13101805

Cited by 9 publications

(2 citation statements)

References 41 publications

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“…According to LD decay, the region 200 kb upstream and downstream of a significant SNP was classified as an LD block. An LD block containing more than two significant SNPs was defined as a QTL [ 55 ]. In each QTL, the SNP with minimum p -value was considered as the lead SNP [ 56 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Association Analysis of Effective Tillers in Rice under Different Nitrogen Gradients

Liu,

Xin,

Chen

et al. 2024

IJMS

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Nitrogen is a crucial element that impacts rice yields, and effective tillering is a significant agronomic characteristic that can influence rice yields. The way that reduced nitrogen affects effective tillering is a complex quantitative trait that is controlled by multiple genes, and its genetic basis requires further exploration. In this study, 469 germplasm varieties were used for a genome-wide association analysis aiming to detect quantitative trait loci (QTL) associated with effective tillering at low (60 kg/hm2) and high (180 kg/hm2) nitrogen levels. QTLs detected over multiple years or under different treatments were scrutinized in this study, and candidate genes were identified through haplotype analysis and spatio-temporal expression patterns. A total of seven genes (NAL1, OsCKX9, Os01g0690800, Os02g0550300, Os02g0550700, Os04g0615700, and Os04g06163000) were pinpointed in these QTL regions, and were considered the most likely candidate genes. These results provide favorable information for the use of auxiliary marker selection in controlling effective tillering in rice for improved yields.

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Section: Methodsmentioning

confidence: 99%

Genome-Wide Association Analysis of Effective Tillers in Rice under Different Nitrogen Gradients

Liu,

Xin,

Chen

et al. 2024

IJMS

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“…Alternatively, linkage disequilibrium (LD) based mapping, also known as genome-wide association study (GWAS), is an efficient and powerful strategy to utilize the natural variation of germplasm and helps in the identification of genomic loci. GWAS is a method of searching the entire genome for phenotypes showing continuous variation and mutations representing associations in natural individuals, or for lines using whole genome sequences [10]. Nowadays, the GWAS has become a prevalent study for the identification of QTLs.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice (Oryza Sativa L.) Using SNPs Markers

Ashfaq

Rasheed

Zhu

et al. 2023

Genes

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Rice (Oryza sativa L.) is a staple food for more than 50% of the world’s population. Rice cultivar improvement is critical in order to feed the world’s growing population. Improving yield is one of the main aims of rice breeders. However, yield is a complex quantitative trait controlled by many genes. The presence of genetic diversity is the key factor to improve the yield hence, the presence of diversity in any germplasm is important for yield improvement. In the current study, the rice germplasm was collected from Pakistan and the United States of America and a panel of 100 diverse genotypes was utilized to identify important yield and yield-related traits. For this, a genome-wide association study (GWAS) was performed to identify the genetic loci related to yield. The GWAS on the diverse germplasm will lead to the identification of new genes which can be utilized in the breeding program for improvement of yield. For this reason, firstly, the germplasm was phenotypically evaluated in two growing seasons for yield and yield-related traits. The analysis of variance results showed significant differences among traits which showed the presence of diversity in the current germplasm. Secondly, the germplasm was also genotypically evaluated using 10K SNP. Genetic structure analysis showed the presence of four groups which showed that enough genetic diversity was present in the rice germplasm to be used for association mapping analysis. The results of GWAS identified 201 significant marker trait associations (MTAs. 16 MTAs were identified for plant height, 49 for days to flowering, three for days to maturity, four for tillers per plant, four for panicle length, eight for grains per panicle, 20 unfilled grains per panicle, 81 for seed setting %, four for thousand-grain weight, five for yield per plot and seven for yield per hectare. Apart from this, some pleiotropic loci were also identified. The results showed that panicle length (PL) and thousand-grain weight (TGW) were controlled by a pleiotropic locus OsGRb23906 on chromosome 1 at 10,116,371 cM. The loci OsGRb25803 and OsGRb15974 on chromosomes 4 and 8 at the position of 14,321,111 cM and 6,205,816 cM respectively, showed pleiotropic effects for seed setting % (SS) and unfilled grain per panicle (UG/P). A locus OsGRb09180 on chromosome 4 at 19,850,601 cM was significantly linked with SS and yield/ha. Furthermore, gene annotation was performed, and results indicated that the 190 candidate genes or QTLs that closely linked with studied traits. These candidate genes and novel significant markers could be useful in marker-assisted gene selection and QTL pyramiding to improve rice yield and the selection of potential parents, recombinants and MTAs which could be used in rice breeding programs to develop high-yielding rice varieties for sustainable food security.

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Mapping and validation of quantitative trait loci associated with dorsal aleurone thickness in rice (Oryza sativa)

Chen

Xue

et al. 2023

Theor Appl Genet

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Development of SNP Markers from GWAS for Selecting Seed Coat and Aleurone Layers in Brown Rice (Oryza sativa L.)

Cited by 9 publications

References 41 publications

Genome-Wide Association Analysis of Effective Tillers in Rice under Different Nitrogen Gradients

Genome-Wide Association Analysis of Effective Tillers in Rice under Different Nitrogen Gradients

Genome-Wide Association Mapping for Yield and Yield-Related Traits in Rice (Oryza Sativa L.) Using SNPs Markers

Mapping and validation of quantitative trait loci associated with dorsal aleurone thickness in rice (Oryza sativa)

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