Genome-wide association studies for agronomical traits in winter rice accessions of Assam

Verma, Rahul Kumar; Chetia, S. K.; Dey, P. C.; Rahman, Anjum; Saikia, Sandhani; Sharma, Vinay; Sharma, Himanshu; Sen, Priyabrata; Modi, Mahendra Kumar

doi:10.1016/j.ygeno.2020.11.033

Cited by 17 publications

(7 citation statements)

References 38 publications

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“…For example, 42 QTNs related to salt stress in wheat were detected using multiple methods (Chaurasia et al, 2020). Hence, environment-stable and method-stable QTNs are more reliable for breeding programs, with similar results reported in other crop plants (Zhang et al, 2019), including soybean (Ikram et al, 2020), maize (Ma et al, 2018), wheat (Chaurasia et al, 2020;Danakumara et al, 2021), and rice (Verma et al, 2021). In addition, the 38 stable QTNs identified in our study are considered novel as they are not located in the genomic region of previously reported QTLs for TBW.…”

Section: Statistical Power Of Multi-locus Genome-wide Association Methods and Significance Of Stable Quantitative Trait Nucleotidessupporting

confidence: 79%

Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Lai

Ikram

et al. 2021

Front. Plant Sci.

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Tobacco bacterial wilt (TBW) is a devastating soil-borne disease threatening the yield and quality of tobacco. However, its genetic foundations are not fully understood. In this study, we identified 126,602 high-quality single-nucleotide polymorphisms (SNPs) in 94 tobacco accessions using genotyping-by-sequencing (GBS) and a 94.56 KB linkage disequilibrium (LD) decay rate for candidate gene selection. The population structure analysis revealed two subpopulations with 37 and 57 tobacco accessions. Four multi-locus genome-wide association study (ML-GWAS) approaches identified 142 quantitative trait nucleotides (QTNs) in E1–E4 and the best linear unbiased prediction (BLUP), explaining 0.49–22.52% phenotypic variance. Of these, 38 novel stable QTNs were identified across at least two environments/methods, and their alleles showed significant TBW-DI differences. The number of superior alleles associated with TBW resistance for each accession ranged from 4 to 24; eight accessions had more than 18 superior alleles. Based on TBW-resistant alleles, the five best cross combinations were predicted, including MC133 × Ruyuan No. 1 and CO258 × ROX28. We identified 52 candidate genes around 38 QTNs related to TBW resistance based on homologous functional annotation and KEGG enrichment analysis, e.g., CYCD3;2, BSK1, Nitab4.5_0000641g0050, Nitab4.5_0000929g0030. To the best of our knowledge, this is the first comprehensive study to identify QTNs, superior alleles, and their candidate genes for breeding TBW-resistant tobacco varieties. The results provide further insight into the genetic architecture, marker-assisted selection, and functional genomics of TBW resistance, improving future breeding efforts to increase crop productivity.

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Section: Statistical Power Of Multi-locus Genome-wide Association Methods and Significance Of Stable Quantitative Trait Nucleotidessupporting

confidence: 79%

Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Lai

Ikram

et al. 2021

Front. Plant Sci.

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“…As spikelet fertility is a major determinant of grain yield 41 , there is a significant positive correlation between spikelet fertility with grain yield. We have observed that some traditional Sali (winter) genotypes from Assam and Joha (aromatic) genotypes have high spikelet fertility.…”

Section: Discussionmentioning

confidence: 99%

Grain iron and zinc content is independent of anthocyanin accumulation in pigmented rice genotypes of Northeast region of India

Gogoi,

Singh,

Swamy

et al. 2024

Sci Rep

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The traditional rice genotypes of Assam are considered to have biological value due to the presence of several bioactive compounds like flavonoids, polyphenols, and anthocyanins, which have antioxidant, anti-cancer, anti-diabetic, and anti-aging properties. The pigmented genotypes are considered to have high iron (Fe) content. However, the effect of Fe and Zinc (Zn) accumulation on anthocyanin content is yet to be studied in pigmented rice of Assam. We studied the Fe, Zn, and anthocyanin content in grains of 204 traditional rice of Assam, which are traditionally preferred for their nutraceutical properties. We performed phenotypic and biochemical compositional analyses of 204 genotypes to identify those having high Fe, Zn, and anthocyanin. We also carried out the differential expression of a few selected Fe and Zn transporter genes along with the expression of anthocyanin biosynthesis genes. Interestingly, all pigmented rice genotypes contained a higher amount of phenolic compound than the non-pigmented form of rice. We found the highest (32.73 g) seed yield per plant for genotype Jengoni followed by Kajoli chokuwa and Khau Pakhi 1. We also listed 30 genotypes having high levels of Fe and Zn content. The genotype Jengoni accumulated the highest (186.9 μg g−1) Fe, while the highest Zn (119.9 μg g−1) content was measured in genotype Bora (Nagaon), The levels of Ferritin 2 gene expression were found to be significantly higher in Bora (Nagaon) (> 2-fold). For Zn accumulation, the genotype DRR Dhan-45, which was released as a high Zn content variety, showed significant up-regulation of the ZIP4 gene at booting (> 7-fold), post-anthesis (7.8-fold) and grain filling (> 5-fold) stages followed by Bora (Nagaon) (> 3-fold) at post-anthesis. Anthocyanidin synthase gene, Flavanone 3-dioxygenase 1-like (FDO1), and Chalcone-flavanone isomerase-like genes were up-regulated in highly pigmented genotype Bora (Nagaon) followed by Jengoni. Based on our data there was no significant correlation between iron and zinc content on the accumulation of anthocyanin. This challenges the present perception of the higher nutritive value in terms of the micronutrient content of the colored rice of Assam. This is the first report on the detailed characterization of traditional rice genotypes inclusive of phenotypic, biochemical, nutritional, and molecular attributes, which would be useful for designing the breeding program to improve Fe, Zn, or anthocyanin content in rice.

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“…With the development of high-throughput sequencing and other biotechnological tools, the GWAS has been verified to be a useful approach for identifying genes, alleles, or haplotypes related to any traits of interest under complex environments. The GWAS has played a pivotal role in identifying many important genes which govern various complex agronomic traits such as flowering time, plant height, and panicle length in rice [ 27 , 28 , 29 , 30 , 31 , 32 ], and particularly starch-related parameters [ 20 , 33 , 34 ]. However, GWAS analysis for the CEQs traits has not been conducted in the Shanlan landrace rice.…”

Section: Introductionmentioning

confidence: 99%

Population Structure and Genetic Diversity of Shanlan Landrace Rice for GWAS of Cooking and Eating Quality Traits

Zhang,

Deng,

Peng

et al. 2024

IJMS

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The Shanlan landrace rice in Hainan Province, China, is a unique upland rice germplasm that holds significant value as a genetic resource for rice breeding. However, its genetic diversity and its usefulness in rice breeding have not been fully explored. In this study, a total of eighty-four Shanlan rice, three typical japonica rice cultivars, and three typical indica rice cultivars were subjected to resequencing of their genomes. As a result, 11.2 million high-quality single nucleotide polymorphisms (SNPs) and 1.6 million insertion/deletions (InDels) were detected. Population structure analysis showed all the rice accessions could be divided into three main groups, i.e., Geng/japonica 1 (GJ1), GJ2, and Xian/indica (XI). However, the GJ1 group only had seven accessions including three typical japonica cultivars, indicating that most Shanlan landrace rice are different from the modern japonica rice. Principal component analysis (PCA) showed that the first three principal components explained 60.7% of the genetic variation. Wide genetic diversity in starch physicochemical parameters, such as apparent amylose content (AAC), pasting viscosity, texture properties, thermal properties, and retrogradation representing the cooking and eating quality was also revealed among all accessions. The genome-wide association study (GWAS) for these traits was conducted and identified 32 marker trait associations in the entire population. Notably, the well-known gene Waxy (Wx) was identified for AAC, breakdown viscosity, and gumminess of the gel texture, and SSIIa was identified for percentage of retrogradation and peak gelatinization temperature. Upon further analysis of nucleotide diversity in Wx, six different alleles, wx, Wxa, Wxb, Wxin, Wxla/mw, and Wxlv in Shanlan landrace rice were identified, indicating rich gene resources in Shanlan rice for quality rice breeding. These findings are expected to contribute to the development of new rice with premium quality.

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Genome-wide association studies for agronomical traits in winter rice accessions of Assam

Cited by 17 publications

References 38 publications

Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Identification of Novel Quantitative Trait Nucleotides and Candidate Genes for Bacterial Wilt Resistance in Tobacco (Nicotiana tabacum L.) Using Genotyping-by-Sequencing and Multi-Locus Genome-Wide Association Studies

Grain iron and zinc content is independent of anthocyanin accumulation in pigmented rice genotypes of Northeast region of India

Population Structure and Genetic Diversity of Shanlan Landrace Rice for GWAS of Cooking and Eating Quality Traits

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