scholarly journals Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat

2018 ◽  
Vol 19 (10) ◽  
pp. 3011 ◽  
Author(s):  
Madhav Bhatta ◽  
Alexey Morgounov ◽  
Vikas Belamkar ◽  
P. Baenziger
Keyword(s):  
Drought Stress ◽  
Grain Yield ◽  
Association Study ◽  
Hexaploid Wheat ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Synthetic Hexaploid Wheat ◽  
Phenotypic Variance ◽  
Genome Wide ◽  
Synthetic Hexaploid

Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x = 14, DD, Aegilops tauschii Coss.) and is reported to have significant novel alleles-controlling biotic and abiotic stresses resistance. A genome-wide association study (GWAS) was conducted to unravel these loci [marker–trait associations (MTAs)] using 35,648 genotyping-by-sequencing-derived single nucleotide polymorphisms in 123 SHWs. We identified 90 novel MTAs (45, 11, and 34 on the A, B, and D genomes, respectively) and haplotype blocks associated with grain yield and yield-related traits including root traits under drought stress. The phenotypic variance explained by the MTAs ranged from 1.1% to 32.3%. Most of the MTAs (120 out of 194) identified were found in genes, and of these 45 MTAs were in genes annotated as having a potential role in drought stress. This result provides further evidence for the reliability of MTAs identified. The large number of MTAs (53) identified especially on the D-genome demonstrate the potential of SHWs for elucidating the genetic architecture of complex traits and provide an opportunity for further improvement of wheat under rapidly changing climatic conditions.

scholarly journals Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

Rice ◽  
2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Chen Liu ◽  
Kai Chen ◽  
Xiuqin Zhao ◽  
Xiaoqian Wang ◽  
Congcong Shen ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Grain Yield ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Field Conditions ◽  
Genome Wide Association ◽  
Saline Stress ◽  
Rice Breeding ◽  
Genome Wide

Abstract Background Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages. Results Large phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms “biological processes” and “molecular function” with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions. Conclusions Using high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.

Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit

Genetica ◽  
2016 ◽  
Vol 144 (6) ◽  
pp. 651-664 ◽  
Author(s):  
Gabriel Feresin Pantalião ◽  
Marcelo Narciso ◽  
Cléber Guimarães ◽  
Adriano Castro ◽  
José Manoel Colombari ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Water Deficit ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

2011 ◽  
Vol 44 (1) ◽  
pp. 32-39 ◽  
Author(s):  
Xuehui Huang ◽  
Yan Zhao ◽  
Xinghua Wei ◽  
Canyang Li ◽  
Ahong Wang ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Flowering Time ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Yield Traits ◽  
Rice Germplasm ◽  
Genome Wide

scholarly journals Genome-wide association study reveals the genetic architecture of 27 yield-related traits in tomato

2020 ◽  
Author(s):  
Jie Ye ◽  
Xin Wang ◽  
Wenqian Wang ◽  
Huiyang Yu ◽  
Guo Ai ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Genetic Research ◽  
Reproductive Development ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Vegetable Crop ◽  
Genome Wide ◽  
Malate Transporter

Abstract Tomato (Solanum lycopersicum) is a highly valuable vegetable crop and yield is one of the most important traits. Uncovering the genetic architecture of yield-related traits in tomato is critical for the management of vegetative and reproductive development, thereby enhancing yield. Here we perform a comprehensive genome-wide association study for 27 yield-related traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many reported and novel genes related to vegetative and reproductive development, were identified, and these loci explained an average of ~8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection, especially during tomato improvement. Furthermore, a candidate gene, SlALMT15 that encodes an aluminum-activated malate transporter, was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation through increasing photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.

scholarly journals Genome-Wide Association Study Reveals Novel Genomic Regions Associated with 10 Grain Minerals in Synthetic Hexaploid Wheat

2018 ◽  
Vol 19 (10) ◽  
pp. 3237 ◽  
Author(s):  
Madhav Bhatta ◽  
P. Baenziger ◽  
Brian Waters ◽  
Rachana Poudel ◽  
Vikas Belamkar ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Synthetic Hexaploid Wheat ◽  
Mineral Concentration ◽  
D Genome ◽  
Favorable Alleles ◽  
Genome Wide ◽  
Synthetic Hexaploid ◽  
Genomic Regions ◽  
Mineral Concentrations

Synthetic hexaploid wheat (SHW; Triticum durum L. × Aegilops tauschii Coss.) is a means of introducing novel genes/genomic regions into bread wheat (T. aestivum L.) and a potential genetic resource for improving grain mineral concentrations. We quantified 10 grain minerals (Ca, Cd, Cu, Co, Fe, Li, Mg, Mn, Ni, and Zn) using an inductively coupled mass spectrometer in 123 SHWs for a genome-wide association study (GWAS). A GWAS with 35,648 single nucleotide polymorphism (SNP) markers identified 92 marker-trait associations (MTAs), of which 60 were novel and 40 were within genes, and the genes underlying 20 MTAs had annotations suggesting a potential role in grain mineral concentration. Twenty-four MTAs on the D-genome were novel and showed the potential of Ae. tauschii for improving grain mineral concentrations such as Ca, Co, Cu, Li, Mg, Mn, and Ni. Interestingly, the large number of novel MTAs (36) identified on the AB genome of these SHWs indicated that there is a lot of variation yet to be explored and to be used in the A and B genome along with the D-genome. Regression analysis identified a positive correlation between a cumulative number of favorable alleles at MTA loci in a genotype and grain mineral concentration. Additionally, we identified multi-traits and stable MTAs and recommended 13 top 10% SHWs with a higher concentration of beneficial grain minerals (Cu, Fe, Mg, Mn, Ni, and Zn), a large number of favorable alleles compared to low ranking genotypes and checks that could be utilized in the breeding program for the genetic biofortification. This study will further enhance our understanding of the genetic architecture of grain minerals in wheat and related cereals.

scholarly journals Genome-wide association study for grain yield and related traits in elite wheat varieties and advanced lines using SNP markers

PLoS ONE ◽  
2017 ◽  
Vol 12 (11) ◽  
pp. e0188662 ◽  
Author(s):  
Sheng-Xing Wang ◽  
Yu-Lei Zhu ◽  
De-Xin Zhang ◽  
Hui Shao ◽  
Peng Liu ◽  
...  
Keyword(s):  
Grain Yield ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Wheat Varieties ◽  
Genome Wide
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