Multi-locus genome-wide association studies reveal novel genomic regions associated with vegetative stage salt tolerance in bread wheat (Triticum aestivum L.)

Genomics ◽  
2020 ◽  
Vol 112 (6) ◽  
pp. 4608-4621
Author(s):  
Shiksha Chaurasia ◽  
Amit Kumar Singh ◽  
L.S. Songachan ◽  
Axma Dutt Sharma ◽  
Rakesh Bhardwaj ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Salt Tolerance ◽  
Bread Wheat ◽  
Association Studies ◽  
Triticum Aestivum L ◽  
Genome Wide Association ◽  
Vegetative Stage ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Genomic Regions

scholarly journals Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yousef Rahimi ◽  
Mohammad Reza Bihamta ◽  
Alireza Taleei ◽  
Hadi Alipour ◽  
Pär K. Ingvarsson
Keyword(s):  
Bread Wheat ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Wheat Varieties ◽  
Data Set ◽  
Protein Coding ◽  
Genome Wide

Abstract Background Identification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS). Genome-wide association studies (GWAS) have increasingly been used as potent tools in identifying marker-trait associations (MTAs). The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or newly developed varieties of wheat to balance supply and demand throughout the world. Landraces collected from different climate zones can be an invaluable resource for such adaptive alleles. Results GWAS was performed using a collection of 298 Iranian bread wheat varieties and landraces to explore the genetic basis of agronomic traits during 2016–2018 cropping seasons under normal (well-watered) and stressed (rain-fed) conditions. A high-quality genotyping by sequencing (GBS) dataset was obtained using either all original single nucleotide polymorphism (SNP, 10938 SNPs) or with additional imputation (46,862 SNPs) based on W7984 reference genome. The results confirm that the B genome carries the highest number of significant marker pairs in both varieties (49,880, 27.37%) and landraces (55,086, 28.99%). The strongest linkage disequilibrium (LD) between pairs of markers was observed on chromosome 2D (0.296). LD decay was lower in the D genome, compared to the A and B genomes. Association mapping under two tested environments yielded a total of 313 and 394 significant (−log10P >3) MTAs for the original and imputed SNP data sets, respectively. Gene ontology results showed that 27 and 27.5% of MTAs of SNPs in the original set were located in protein-coding regions for well-watered and rain-fed conditions, respectively. While, for the imputed data set 22.6 and 16.6% of MTAs represented in protein-coding genes for the well-watered and rain-fed conditions, respectively. Conclusions Our finding suggests that Iranian bread wheat landraces harbor valuable alleles that are adaptive under drought stress conditions. MTAs located within coding genes can be utilized in genome-based breeding of new wheat varieties. Although imputation of missing data increased the number of MTAs, the fraction of these MTAs located in coding genes were decreased across the different sub-genomes.

scholarly journals Identification of Loci Controlling the Dwarfism Trait in the White Sailfin Molly (Poecilia latipinna) Using Genome-Wide Association Studies Based on Genotyping-By-Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 418
Author(s):  
Fan Shao ◽  
Jing Liu ◽  
Mengyuan Ren ◽  
Junying Li ◽  
Haigang Bao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Expression Level ◽  
Genome Wide Association Studies ◽  
Sailfin Molly ◽  
Genome Wide ◽  
Genomic Regions ◽  
Sailfin Mollies

Dwarfism is a condition defined by low harvest weight in fish, but also results in strange body figures which may have potential for the selective breeding of new ornamental fish strains. The objectives of this study are to reveal the physiological causes of dwarfism and identify the genetic loci controlling this trait in the white sailfin molly. Skeletons of dwarf and normal sailfin mollies were observed by X-ray radioscopy and skeletal staining. Genome-wide association studies based on genotyping-by-sequencing (n = 184) were used to map candidate genomic regions associated with the dwarfism trait. Quantitative real-time PCR was performed to determine the expression level of candidate genes in normal (n = 8) and dwarf (n = 8) sailfin mollies. We found that the dwarf sailfin molly has a short and dysplastic spine in comparison to the normal fish. Two regions, located at NW_015112742.1 and NW_015113621.1, were significantly associated with the dwarfism trait. The expression level of three candidate genes, ADAMTS like 1, Larp7 and PPP3CA, were significantly different between the dwarf and normal sailfin mollies in the hepatopancreas, with PPP3CA also showing significant differences in the vertebrae and Larp7 showing significant differences in the muscle. This study identified genomic regions and candidate genes associated with the dwarfism trait in the white sailfin molly and would provide a reference to determine dwarf-causing variations.

Genome-wide association analyses of common wheat (Triticum aestivum L.) germplasm identifies multiple loci for aluminium resistanceThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 957-966 ◽  
Author(s):  
Harsh Raman ◽  
Benjamin Stodart ◽  
Peter R. Ryan ◽  
Emmanuel Delhaize ◽  
Livinus Emebiri ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Association Mapping ◽  
Common Wheat ◽  
Acid Soils ◽  
Triticum Aestivum L ◽  
Genome Wide Association ◽  
Phenotypic Variance ◽  
Association Analyses ◽  
Genome Wide ◽  
Genomic Regions

Aluminium (Al3+) toxicity restricts productivity and profitability of wheat ( Triticum aestivum L.) crops grown on acid soils worldwide. Continued gains will be obtained by identifying superior alleles and novel Al3+ resistance loci that can be incorporated into breeding programs. We used association mapping to identify genomic regions associated with Al3+ resistance using 1055 accessions of common wheat from different geographic regions of the world and 178 polymorphic diversity arrays technology (DArT) markers. Bayesian analyses based on genetic distance matrices classified these accessions into 12 subgroups. Genome-wide association analyses detected markers that were significantly associated with Al3+ resistance on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5B, 6A, 6B, 7A, and 7B. Some of these genomic regions correspond to previously identified loci for Al3+ resistance, whereas others appear to be novel. Among the markers targeting TaALMT1 (the major Al3+-resistance gene located on chromosome 4D), those that detected alleles in the promoter explained most of the phenotypic variance for Al3+ resistance, which is consistent with this region controlling the level of TaALMT1 expression. These results demonstrate that genome-wide association mapping cannot only confirm known Al3+-resistance loci, such as those on chromsomes 4D and 4B, but they also highlight the utility of this technique in identifying novel resistance loci.

scholarly journals Genome-wide association studies to identify rice salt-tolerance markers

2017 ◽  
Vol 41 (5) ◽  
pp. 970-982 ◽  
Author(s):  
Juan Patishtan ◽  
Tom N. Hartley ◽  
Raquel Fonseca de Carvalho ◽  
Frans J.M. Maathuis
Keyword(s):  
Salt Tolerance ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Genome-Wide Association Studies in Indian Buffalo Revealed Genomic Regions for Lactation and Fertility

2021 ◽  
Vol 12 ◽  
Author(s):  
Vikas Vohra ◽  
Supriya Chhotaray ◽  
Gopal Gowane ◽  
Rani Alex ◽  
Anupama Mukherjee ◽  
...  
Keyword(s):  
Milk Yield ◽  
Milk Fat ◽  
Association Studies ◽  
Post Partum ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Improvement Programs ◽  
Genomic Regions ◽  
Fertility Traits

Murrah breed of buffalo is an excellent dairy germplasm known for its superior milk quality in terms of milk fat and solids-not-fat (SNF); however, it is often reported that Indian buffaloes had lower lactation and fertility potential compared to the non-native cattle of the country. Recent techniques, particularly the genome-wide association studies (GWAS), to identify genomic variations associated with lactation and fertility traits offer prospects for systematic improvement of buffalo. DNA samples were sequenced using the double-digestion restriction-associated DNA (RAD) tag genotyping-by-sequencing. The bioinformatics pipeline was standardized to call the variants, and single-nucleotide polymorphisms (SNPs) qualifying the stringent quality check measures were retained for GWAS. Over 38,000 SNPs were used to perform GWAS on the first two principal components of test-day records of milk yields, fat percentages, and SNF percentages, separately. GWAS was also performed on 305 days’ milk yield; lactation persistency was estimated through the rate of decline after attaining the peak yield method, along with three other standard methods; and breeding efficiency, post-partum breeding interval, and age at sexual maturity were considered fertility traits. Significant association of SNPs was observed for the first principal component, explaining the maximum proportion of variation in milk yield. Furthermore, some potential genomic regions were identified to have a potential role in regulating milk yield and fertility in Murrah. Identification of such genomic regions shall help in carrying out an early selection of high-yielding persistent Murrah buffaloes and, in the long run, would be helpful in shaping their future genetic improvement programs.

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