scholarly journals DArTseq Genotypic and Phenotypic Diversity of Barley Landraces Originating from Different Countries

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2330
Author(s):  
Joanna Dziurdziak ◽  
Grzegorz Gryziak ◽  
Jolanta Groszyk ◽  
Wiesław Podyma ◽  
Maja Boczkowska
Keyword(s):  
Phenotypic Diversity ◽  
Spring Barley ◽  
Small Region ◽  
Special Collections ◽  
Genome Wide ◽  
Variable Level ◽  
A Genome ◽  
Health Promoting ◽  
Barley Landraces ◽  
Pure Lines

Landraces are considered a key element of agrobiodiversity because of their high variability and adaptation to local environmental conditions, but at the same time, they represent a breeding potential hidden in gene banks that has not yet been fully appreciated and utilized. Here, we present a genome-wide DArTseq analysis of the diversity of 116 spring barley landraces preserved in the collection of the Polish gene bank. Genetic analysis revealed considerable variation in this collection and several distinct groups related to the landraces’ country of origin and the grain type were identified. The genetic distinctness of hulless accessions may provide a basis for pro-quality breeding aimed at functional food production. However, the variable level of accession heterogeneity can be a significant obstacle. A solution to this problem is the establishment of special collections composed of pure lines that are accessible to breeders. Regions lacking genetic diversity have also been identified on 1H and 4H chromosomes. A small region of reduced heterogeneity was also present in the hulless forms in the vicinity of the nud gene that determines the hulless grain type. However, the SNPs present in this area may also be important in selection for traits related to grain weight and size because their QTLs were found there. This may support breeding of hulless forms of spring barley which may have applications in the production of high-quality foods with health-promoting values.

scholarly journals A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain

PLoS ONE ◽  
2017 ◽  
Vol 12 (8) ◽  
pp. e0182537 ◽  
Author(s):  
Ali Saleh Hassan ◽  
Kelly Houston ◽  
Jelle Lahnstein ◽  
Neil Shirley ◽  
Julian G. Schwerdt ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Spring Barley ◽  
Barley Grain ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Association Study in Wheat Identifies Resistance to the Cereal Cyst Nematode Heterodera filipjevi

2016 ◽  
Vol 106 (10) ◽  
pp. 1128-1138 ◽  
Author(s):  
Shree R. Pariyar ◽  
Abdelfattah A. Dababat ◽  
Wiebke Sannemann ◽  
Gul Erginbas-Orakci ◽  
Abdelnaser Elashry ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Phenotypic Diversity ◽  
Cyst Nematode ◽  
Genome Wide Association ◽  
Cyst Nematodes ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
A Genome ◽  
Heterodera Filipjevi

The cyst nematode Heterodera filipjevi is a plant parasite causing substantial yield loss in wheat. Resistant cultivars are the preferred method of controlling cyst nematodes. Association mapping is a powerful approach to detect associations between phenotypic variation and genetic polymorphisms; in this way favorable traits such as resistance to pathogens can be located. Therefore, a genome-wide association study of 161 winter wheat accessions was performed with a 90K iSelect single nucleotide polymorphism (SNP) chip. Population structure analysis grouped into two major subgroups and first principal component accounted 6.16% for phenotypic diversity. The genome-wide linkage disequilibrium across wheat was 3 cM. Eleven quantitative trait loci (QTLs) on chromosomes 1AL, 2AS, 2BL, 3AL, 3BL, 4AS, 4AL, 5BL, and 7BL were identified using a mixed linear model false discovery rate of P < 0.01 that explained 43% of total genetic variation. This is the first report of QTLs conferring resistance to H. filipjevi in wheat. Eight QTLs on chromosomes 1AL, 2AS, 2BL, 3AL, 4AL, and 5BL were linked to putative genes known to be involved in plant−pathogen interactions. Two other QTLs on 3BL and one QTL on 7BL linked to putative genes known to be involved in abiotic stress.

scholarly journals Genome wide association study of agronomic and seed traits in a world collection of proso millet (Panicum miliaceum L.)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sameh Boukail ◽  
Mercy Macharia ◽  
Mara Miculan ◽  
Alberto Masoni ◽  
Alessandro Calamai ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Phenotypic Diversity ◽  
Genome Wide Association ◽  
Seed Traits ◽  
Proso Millet ◽  
Genome Wide ◽  
World Collection ◽  
A Genome ◽  
Western Asia

Abstract Background The climate crisis threatens sustainability of crop production worldwide. Crop diversification may enhance food security while reducing the negative impacts of climate change. Proso millet (Panicum milaceum L.) is a minor cereal crop which holds potential for diversification and adaptation to different environmental conditions. In this study, we assembled a world collection of proso millet consisting of 88 varieties and landraces to investigate its genomic and phenotypic diversity for seed traits, and to identify marker-trait associations (MTA). Results Sequencing of restriction-site associated DNA fragments yielded 494 million reads and 2,412 high quality single nucleotide polymorphisms (SNPs). SNPs were used to study the diversity in the collection and perform a genome wide association study (GWAS). A genotypic diversity analysis separated accessions originating in Western Europe, Eastern Asia and Americas from accessions sampled in Southern Asia, Western Asia, and Africa. A Bayesian structure analysis reported four cryptic genetic groups, showing that landraces accessions had a significant level of admixture and that most of the improved proso millet materials clustered separately from landraces. The collection was highly diverse for seed traits, with color varying from white to dark brown and width spanning from 1.8 to 2.6 mm. A GWAS study for seed morphology traits identified 10 MTAs. In addition, we identified three MTAs for agronomic traits that were previously measured on the collection. Conclusion Using genomics and automated seed phenotyping, we elucidated phylogenetic relationships and seed diversity in a global millet collection. Overall, we identified 13 MTAs for key agronomic and seed traits indicating the presence of alleles with potential for application in proso breeding programs.

scholarly journals Genome-wide association studies uncover candidate genes for Zinc, Iron, and Selenium concentration in barley grains

2021 ◽  
Author(s):  
Samar G. Thabet ◽  
Dalia Z. Alomari ◽  
Ahmad M. Alqudah
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Spring Barley ◽  
Genome Wide Association ◽  
Human Consumption ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
A Genome ◽  
Barley Grains

Abstract Background Barley (Hordeum vulgare L.) is one of the most important staple food crops worldwide. Mineral concentrations in cereals are important for human health; hence improving Zn, Fe and Se accumulation in grains is an imperative need. This study was designed to understand the genetic architecture of Zn, Fe and Se grain concentrations in barley grains. Results We performed a genome-wide association study (GWAS) for grain Zn, Fe and Se concentrations in 216 spring barley accessions, using field data from 2 years. All the accessions were genotyped with a high-density 9K SNPs array from IlluminaTM. The mean values of estimated BLUEs for Zn, Fe and Se were 38.37, 35.56 and 39.45 µg g− 1 dry weight, respectively. High heritability was equaled 75.65% for Fe across the two environments, while moderate heritability values were detected for Zn and Se. Notably, wide genetic variation was found among genotypes for Zn, Fe and Se concentrations. A total of 222 SNPs associated with Zn, Fe and Se were detected on all chromosomes, where the highest significant associations is linked to Fe accumulation. Three genomic regions include newly identified putative candidate genes, which are related to Zn uptake and transport or represent Homeobox leucine zipper protein. Additionally, several significant associations were physically located inside or near genes which are potentially involved in Zn and Fe homoeostasis of which two candidate genes at 5H (502,454,312–502,455,148 bp) and 7H (205,216,091–205,221,133 bp) were found to be involved in Basic helix loop helix (BHLH) family transcription factor and Squamosa promoter binding-like protein, respectively. Conclusions These findings provide new insights into the genetic basis of Zn, Fe and Se concentration in barley grains that in turn may help plant breeders to select high Zn, Fe and Se-containing genotypes to improve human consumption and grain quality.

Establishment of a genome-wide RNAi screen; Identification of novel genes involved in clonal maintenance of ALL

2014 ◽  
Vol 226 (03) ◽  
Author(s):  
F Ponthan ◽  
D Pal ◽  
J Vormoor ◽  
O Heidenreich
Keyword(s):  
Rnai Screen ◽  
Novel Genes ◽  
Genome Wide ◽  
A Genome

A genome-wide linkage scan for familial partial lipodystrophy susceptibility genes in a German kindreds

2007 ◽  
Vol 30 (4) ◽  
pp. 86
Author(s):  
M. Lanktree ◽  
J. Robinson ◽  
J. Creider ◽  
H. Cao ◽  
D. Carter ◽  
...  
Keyword(s):  
Subcutaneous Fat ◽  
Visceral Obesity ◽  
Fat Distribution ◽  
Dominant Negative ◽  
Molecular Forms ◽  
Partial Lipodystrophy ◽  
Genome Wide ◽  
A Genome ◽  
Familial Partial Lipodystrophy ◽  
Promoter Mutations

Background: In Dunnigan-type familial partial lipodystrophy (FPLD) patients are born with normal fat distribution, but subcutaneous fat from extremities and gluteal regions are lost during puberty. The abnormal fat distribution leads to the development of metabolic syndrome (MetS), a cluster of phenotypes including hyperglycemia, dyslipidemia, hypertension, and visceral obesity. The study of FPLD as a monogenic model of MetS may uncover genetic risk factors of the common MetS which affects ~30% of adult North Americans. Two molecular forms of FPLD have been identified including FPLD2, resulting from heterozygous mutations in the LMNA gene, and FPLD3, resulting from both heterozygous dominant negative and haploinsufficiency mutations in the PPARG gene. However, many patients with clinically diagnosed FPLD have no mutation in either LMNA or PPARG, suggesting the involvement of additional genes in FPLD etiology. Methods: Here, we report the results of an Affymetrix 10K GeneChip microarray genome-wide linkage analysis study of a German kindred displaying the FPLD phenotype and no known lipodystrophy-causing mutations. Results: The investigation identified three chromosomal loci, namely 1q, 3p, and 9q, with non-parametric logarithm of odds (NPL) scores >2.7. While not meeting the criteria for genome-wide significance, it is interesting to note that the 1q and 3p peaks contain the LMNA and PPARG genes respectively. Conclusions: Three possible conclusions can be drawn from these results: 1) the peaks identified are spurious findings, 2) additional genes physically close to LMNA, PPARG, or within 9q, are involved in FPLD etiology, or 3) alternative disease causing mechanisms not identified by standard exon sequencing approaches, such as promoter mutations, alternative splicing, or epigenetics, are also responsible for FPLD.

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