Rapid Identification of QTL for Mesocotyl Length in Rice Through Combining QTL-seq and Genome-Wide Association Analysis

Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F2 populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or G-value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3–14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, Indel-Chr1:18932318 and Indel-Chr7:15404166 for loci qML1.3 and qML7.2 respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding.

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Genome-Wide Association Analysis for Liveweight Traits in Braunvieh Cattle

10.21203/rs.3.rs-485005/v1 ◽

2021 ◽

Author(s):

José Luis Zepeda-Batista ◽

Rafael Nuñez-Domínguez ◽

Rodolfo Ramírez-Valverde ◽

Agustín Ruíz-Flores ◽

Francisco Joel Jahuey-Martínez ◽

...

Keyword(s):

Association Analysis ◽

Genome Wide Association Study ◽

Transmembrane Protein ◽

Tissue Growth ◽

Genome Wide Association ◽

Future Research ◽

Minichromosome Maintenance ◽

Phenotypic Data ◽

Genome Wide ◽

A Genome

Abstract A genome-wide association study (GWAS) for liveweight traits of Braunvieh cattle was performed. The study included 300 genotyped animals by the GeneSeek® Genomic Profiler Bovine LDv.4 panel; after quality control, 22,734 SNP and 276 animals were maintained in the analysis. The examined phenotypic data considered birth, weaning, and yearling weights. The association analysis was performed using the principal components method via the egscore function of the GenABEL version 1.8-0 package in the R environment. The marker rs133262280 located in BTA 22 was associated with birth weight, and two SNPs were associated with weaning weight, rs43668789 (BTA 11) and rs136155567 (BTA 27). New QTL associated with these liveweight traits and four positional and functional candidate genes potentially involved in variations of the analyzed traits were identified. The most important genes in these genomic regions were MCM2 (minichromosome maintenance complex component 2), TPRA1 (transmembrane protein adipocyte associated 1), GALM (galactose mutarotase), and NRG1 (neuregulin 1), with relationships with embryonic cleavage, bone and tissue growth, cell adhesion, and organic development. This study is the first to present a GWAS conducted in Braunvieh cattle in Mexico and represents a basis for future research. Further analyses of found associated regions will clarify its contribution to the genetic basis of growth-related traits.

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Genome-Wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions

Genes ◽

10.3390/genes11010049 ◽

2019 ◽

Vol 11 (1) ◽

pp. 49 ◽

Cited By ~ 3

Author(s):

Hongyan Liu ◽

Junhui Zhan ◽

Jiaolong Li ◽

Xiang Lu ◽

Jindong Liu ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Oryza Sativa L ◽

Seedling Emergence ◽

Culture Conditions ◽

Genome Wide Association ◽

Pcr Analysis ◽

Genome Wide ◽

Mesocotyl Elongation ◽

Direct Seeded

Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice.

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