Dissection of the genetic variation and candidate genes of lint percentage by a genome-wide association study in upland cotton

2019 ◽  
Vol 132 (7) ◽  
pp. 1991-2002 ◽  
Author(s):  
Chengxiang Song ◽  
Wei Li ◽  
Xiaoyu Pei ◽  
Yangai Liu ◽  
Zhongying Ren ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Association Study ◽  
Candidate Genes ◽  
Upland Cotton ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Lint Percentage ◽  
Genome Wide ◽  
A Genome

A genome-wide association study uncovers novel genomic regions and candidate genes of yield-related traits in upland cotton

2018 ◽  
Vol 131 (11) ◽  
pp. 2413-2425 ◽  
Author(s):  
Zhengwen Sun ◽  
Xingfen Wang ◽  
Zhengwen Liu ◽  
Qishen Gu ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Upland Cotton ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

scholarly journals Genome-wide Association Study Reveals Novel Quantitative Trait Loci and Candidate Genes of Lint Percentage in Upland Cotton Based on the CottonSNP80K Array

2021 ◽  
Author(s):  
Yu Chen ◽  
Yang Gao ◽  
Pengyun Chen ◽  
Juan Zhou ◽  
Chuanyun Zhang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Upland Cotton ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Oilseed Crop ◽  
Cotton Production ◽  
Lint Percentage ◽  
Genome Wide

Abstract Cotton (Gossypium spp.) is an important natural textile fiber and oilseed crop widely cultivated in the world. Lint percentage (LP, %) is one of the important yield factor, thus increasing lint percentage is a core goal of cotton breeding improvement. However, the underlying genetic and molecular mechanisms that control lint percentage in upland cotton remain largely unknown. Here, we performed a Genome-wide association study (GWAS) for LP based on phenotypic tests of 254 upland cotton accessions in four environments and BLUPs using the high-density CottonSNP80K array. A total of 41,413 high-quality single-nucleotide polymorphisms (SNPs) were screened and 34 SNPs within 22 QTLs were identified as significantly associated with lint percentage trait in different environments. In total, 175 candidate genes were identified from two major genomic loci (GR1 and GR2) of upland cotton and 50 hub genes were identified through GO enrichment and WGCNA analysis. Furthermore, two candidate/causal genes, Gh_D01G0162 and Gh_D07G0463, which pleiotropically increased lint percentage were identified and further verified its function through LD blocks, haplotypes and qRT-PCR analysis. Co-expression network analysis showed that the candidate/causal and hub gene, Gh_D07G0463, was significantly related to another candidate gene, Gh_D01G0162, and the simultaneous pyramid of the two genes lays the foundation for a more efficient increase in cotton production. Our study provides crucial insights into the genetic and molecular mechanisms underlying variations of yield traits and serves as an important foundation for lint percentage improvement via marker-assisted breeding.

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

scholarly journals Evaluation of candidate genes in a genome-wide association study of childhood asthma in Mexicans

2010 ◽  
Vol 125 (2) ◽  
pp. 321-327.e13 ◽  
Author(s):  
Hao Wu ◽  
Isabelle Romieu ◽  
Min Shi ◽  
Dana B. Hancock ◽  
Huiling Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Childhood Asthma ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

2018 ◽  
Vol 19 (10) ◽  
pp. 3145 ◽  
Author(s):  
Jie Yu ◽  
Weiguo Zhao ◽  
Wei Tong ◽  
Qiang He ◽  
Min-Young Yoon ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Rice Genome ◽  
Genome Wide Association ◽  
Phenotypic Correlation ◽  
Genome Wide ◽  
A Genome ◽  
Germination Stage

Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.

scholarly journals Genetic variation associated with chromosomal aberration frequency: A genome-wide association study

2018 ◽  
Vol 60 (1) ◽  
pp. 17-28 ◽  
Author(s):  
Yasmeen Niazi ◽  
Hauke Thomsen ◽  
Bozena Smolkova ◽  
Ludmila Vodickova ◽  
Sona Vodenkova ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Association Study ◽  
Chromosomal Aberration ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Aberration Frequency ◽  
Genome Wide ◽  
A Genome

scholarly journals A genome‐wide association study of early‐maturation traits in upland cotton based on the CottonSNP80K array

2018 ◽  
Vol 60 (10) ◽  
pp. 970-985 ◽  
Author(s):  
Chengqi Li ◽  
Yuanyuan Wang ◽  
Nijiang Ai ◽  
Yue Li ◽  
Jiafeng Song
Keyword(s):  
Association Study ◽  
Upland Cotton ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Early Maturation ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Association Study for Maize Leaf Cuticular Conductance Identifies Candidate Genes Involved in the Regulation of Cuticle Development

2020 ◽  
Vol 10 (5) ◽  
pp. 1671-1683 ◽  
Author(s):  
Meng Lin ◽  
Susanne Matschi ◽  
Miguel Vasquez ◽  
James Chamness ◽  
Nicholas Kaczmar ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Crop Productivity ◽  
Genome Wide Association ◽  
Cell Wall Modification ◽  
Major Barrier ◽  
Maize Leaf ◽  
Genome Wide ◽  
A Genome

The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study of gc of adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA, in 2016 and 2017). Five genomic regions significantly associated with gc were resolved to seven plausible candidate genes (ISTL1, two SEC14 homologs, cyclase-associated protein, a CER7 homolog, GDSL lipase, and β-D-XYLOSIDASE 4). These candidates are potentially involved in cuticle biosynthesis, trafficking and deposition of cuticle lipids, cutin polymerization, and cell wall modification. Laser microdissection RNA sequencing revealed that all these candidate genes, with the exception of the CER7 homolog, were expressed in the zone of the expanding adult maize leaf where cuticle maturation occurs. With direct application to genetic improvement, moderately high average predictive abilities were observed for whole-genome prediction of gc in locations (0.46 and 0.45) and across all environments (0.52). The findings of this study provide novel insights into the genetic control of gc and have the potential to help breeders more effectively develop drought-tolerant maize for target environments.

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