Identification of QTL TGW12 responsible for grain weight in rice based on recombinant inbred line population crossed by wild rice (Oryza minuta) introgression line K1561 and indica rice G1025

Li, Xiao-Qiong; Yu, Wei; Li, Jun; Yang, Fangwen; Chen, Ying; Chen, Yinghua; Guo, Shan; Sha, Aihua

doi:10.1186/s12863-020-0817-x

Cited by 16 publications

(10 citation statements)

References 42 publications

(25 reference statements)

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“…As we mentioned earlier, three lead SNP loci in chromosome 5 (chr05_9776079, chr05_1025757, and chr05_23772096) were significantly associated with both GWT and GL. As was observed for GL and GW, our association study on GWT presents some congruent results with respect to the previous studies [29, 30], in addition to revealing new chromosomal regions associated with GWT.…”

Section: Resultssupporting

confidence: 89%

Genome Wide Association Studies on 7 Yield-related Traits of 183 Rice Varieties in Bangladesh

Roy¹,

Kabir

Zahan

et al. 2020

Preprint

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Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed Genome Wide Association Studies (GWAS) on 7 rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width and leaf angle) based on 39,40,165 single nucleotide polymorphisms (SNPs) in a population of 183 rice landraces of Bangladesh. Our studies reveal various chromosomal regions that are significantly associated with different traits in Bangladeshi rice varieties. We also identified various candidate genes, which are associated with these traits. This study reveals multiple candidate genes within short intervals. We also identified SNP loci, which are significantly associated with multiple yield-related traits. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. This is the first known GWAS study on various yield-related traits in the varieties of Oryza sativa available in Bangladesh – the fourth largest rice producing country. We believe this study will accelerate rice genetics research and breeding stable high-yielding rice in Bangladesh.

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Section: Resultssupporting

confidence: 89%

Genome Wide Association Studies on 7 Yield-related Traits of 183 Rice Varieties in Bangladesh

Roy¹,

Kabir

Zahan

et al. 2020

Preprint

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“…Based on these or similar studies, many TGW-associated genes of rice have been cloned, such as the RING-type E3 ubiquitin ligase OsGW2 ( Song et al, 2007 ), the arginine-rich domain nuclear protein OsGW5 ( Shomura et al, 2008 ), the SBP domain transcription factor OsGW8 ( Wang et al, 2012 ), and the indole-3-acetic acid (IAA)-glucose hydrolase protein OsTGW6 ( Ishimaru et al, 2013 ). To date, QTLs/genes associated with TGW have been mostly cloned from cultivated rice ( Li et al, 2020 ). Compared with related research in rice, the QTLs and molecular cloning of genes associated with TGW are lacking for maize ( Guo et al, 2011 ; Liu et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Identifying Quantitative Trait Loci for Thousand Grain Weight in Eggplant by Genome Re-Sequencing Analysis

Qian

et al. 2022

Front. Genet.

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Eggplant (Solanum melongena L.; 2n = 24) is one of the most important Solanaceae vegetables and is primarily cultivated in China (approximately 42% of world production) and India (approximately 39%). Thousand-grain weight (TGW) is an important trait that affects eggplant breeding cost and variety promotion. This trait is controlled by quantitative trait loci (QTLs); however, no quantitative trait loci (QTL) has been reported for TGW in eggplant so far, and its potential genetic basis remain unclear. In this study, two eggplant lines, 17C01 (P1, wild resource, small seed) and 17C02 (P2, cultivar, large seed), were crossed to develop F1, F2 (308 lines), BC1P1 (44 lines), and BC1P2 (44 lines) populations for quantitative trait association analysis. The TGWs of P1, P2 and F1 were determined as 3.00, 3.98 and 3.77 g, respectively. The PG-ADI (polygene-controlled additive-dominance-epistasis) genetic model was identified as the optimal model for TGW and the polygene heritability value in the F2 generation was as high as 80.87%. A high-quality genetic linkage bin map was constructed with resequencing analysis. The map contained 3,918 recombination bins on 12 chromosomes, and the total length was 1,384.62 cM. A major QTL (named as TGW9.1) located on chromosome 9 was identified to be strongly associated with eggplant TGW, with a phenotypic variance explanation of 20.51%. A total of 45 annotated genes were identified in the genetic region of TGW9.1. Based on the annotation of Eggplant genome V3 and orthologous genes in Arabidopsis thaliana, one candidate gene SMEL_009g329850 (SmGTS1, encoding a putative ubiquitin ligase) contains 4 SNPs and 2 Indels consecutive intron mutations in the flank of the same exon in P1. SmGTS1 displayed significantly higher expression in P1 and was selected as a potential candidate gene controlling TGW in eggplant. The present results contribute to shed light on the genetic basis of the traits exploitable in future eggplant marker-assisted selection (MAS) breeding.

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“…Grain weight is a synthetic reflect of grain length, width, thickness and plumpness. All these traits have been comprehensively studied using bi-parental populations through QTL mapping (Xing et al 2002;Li et al 2004Li et al , 2020Weng et al 2008;Wang et al 2011;Tang et al 2013;Xu et al 2015;Dong et al 2018;Bazrkar-Khatibani et al 2019), and hundreds of QTLs related to these traits were reported and stored in the Gramene QTL Database (Gupta et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Association Mapping of Thousand Grain Weight using SSR and SNP Markers in Rice (Oryza sativa L.) Across Six Environments

Chen

Dang

Wang

et al. 2021

Tropical Plant Biol.

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Thousand grain weight (TGW) is an important determinant of rice yield, and correlates with grain size, plumpness and grain number per panicle. In rice, there are fewer association mapping studies relating grain weight traits using both SSR and SNP markers. In this study, in order to find robust SSR markers associated with TGW trait and mine elite accessions in rice, we investigated the TGW trait across six environments using a natural population consisted of 462 accessions, and then performed association mapping using both SSR and SNP markers. Using the six datasets from the six environments and their best linear unbiased estimator, we identified eight TGW associated SSR markers, with three environmentally stable and one newly found, on five chromosomes. The associated markers have genetic effect from 3.44% to 20.84%, and two of them carry stable elite allele with positive effect across different environments. Candidate interval association mapping using re-sequencing derived SNP/InDel markers further confirms the TGW-SSR association, and also suggests that 3 TGW-SSR associations were high confident in intervals of size from 176 to 603 kb. These results not only shed more lights on the genetics of TGW trait, but also suggest that the multi-allelic SSR markers should be used as an alternative power tool in gene or QTL mapping.

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Identification of QTL TGW12 responsible for grain weight in rice based on recombinant inbred line population crossed by wild rice (Oryza minuta) introgression line K1561 and indica rice G1025

Cited by 16 publications

References 42 publications

Genome Wide Association Studies on 7 Yield-related Traits of 183 Rice Varieties in Bangladesh

Genome Wide Association Studies on 7 Yield-related Traits of 183 Rice Varieties in Bangladesh

Identifying Quantitative Trait Loci for Thousand Grain Weight in Eggplant by Genome Re-Sequencing Analysis

Association Mapping of Thousand Grain Weight using SSR and SNP Markers in Rice (Oryza sativa L.) Across Six Environments

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