scholarly journals Genome scan identifies flowering-independent effects of barley HsDry2.2 locus on yield traits under water deficit

2017 ◽  
Author(s):  
Lianne Merchuk-Ovnat ◽  
Roi Silberman ◽  
Efrat Laiba ◽  
Andreas Maurer ◽  
Klaus Pillen ◽  
...  
Keyword(s):  
Flowering Time ◽  
Water Deficit ◽  
Genome Wide Association Study ◽  
Grain Filling ◽  
Genotype By Environment Interactions ◽  
Shoot Morphology ◽  
Genotype By Environment ◽  
A Genome ◽  
Wild Allele ◽  
Novel Alleles

AbstractIncreasing crop productivity under climate change requires the identification, selection and utilization of novel alleles for breeding. We analyzed the genotype and field phenotype of the barley HEB-25 multi-parent mapping population under well-watered and water-limited (WW and WL) environments for two years. A genome-wide association study (GWAS) for genotype by-environment interactions was performed for ten traits including flowering time (HEA), plant grain yield (PGY). Comparison of the GWAS for traits per-se to that for QTL-by-environment interactions (QxE), indicates the prevalence of QxE mostly for reproductive traits. One QxE locus on chromosome 2, Hordeum spontaneum Dry2.2 (HsDry2.2), showed a positive and conditional effect on PGY and grain number (GN). The wild allele significantly reduced HEA, however this earliness was not conditioned by water deficit. Furthermore, BC2F1 lines segregating for the HsDry2.2 showed the wild allele confers an advantage over the cultivated in PGY, GN and harvest index as well as modified shoot morphology, longer grain filling period and reduced senescence (only under drought), therefore suggesting adaptation mechanism against water deficit other than escape. This study highlights the value of evaluating wild relatives in search of novel alleles and clues to resilience mechanism underlying crop adaptation to abiotic stress.HighlightA flowering-time independent reproductive advantage of wild over cultivated allele under drought identified in a barley GWAS for genotype-by-environment interactions, with modified shoot morphology, reduced senescence and longer grain filling

scholarly journals Analysis of genotype by environment interactions in a maize mapping population

2021 ◽  
Author(s):  
Asher I Hudson ◽  
Sarah G Odell ◽  
Pierre Dubreuil ◽  
Marie-Helene Tixier ◽  
Sebastien Praud ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Crop Breeding ◽  
Genotype By Environment Interactions ◽  
Genotype By Environment ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Covariances

Genotype by environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype by environment interaction in a maize multi-parent advanced generation intercross population grown across five environments. We found that genotype by environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. In order to understand how genetic correlations between traits change across environments, we estimated the genetic variance-covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype by environment variance. We also performed a genome-wide association study to identify markers associated with genotype by environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype by environment interactions in this population.

scholarly journals Genomic Regions Associated with the Control of Flowering Time in Durum Wheat

2020 ◽  
Author(s):  
Priyanka Gupta ◽  
Hafssa Kabbaj ◽  
Khaoula El Hassouni ◽  
Marco Maccaferri ◽  
Miguel Sabchez-Garcia ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Flowering Time ◽  
Genome Wide Association Study ◽  
Strong Association ◽  
Triticum Aestivum L ◽  
Day Length ◽  
Significant Qtls ◽  
A Genome ◽  
Days To Heading ◽  
Genomic Regions

Flowering time is a critical stage for crop development as it regulates the ability of plants to adapt to an environment. To understand the genetic control of flowering time, a genome wide association study (GWAS) was conducted to identify the genomic regions associated with the control of this trait in durum wheat (Triticum durum Desf.). A total of 96 landraces and 288 modern lines were evaluated for days to heading, growing degree days, and accumulated day length at flowering across 13 environments spread across Morocco, Lebanon, Mauritania, and Senegal. These environments were grouped into four pheno-environments based on temperatures, day length and other climatic variables. Genotyping with 35K Axiom array generated 7,652 polymorphic SNPs in addition to 3 KASP markers associated to known flowering genes. In total, 34 significant QTLs were identified in both landraces and modern lines. Some QTLs had strong association with already known regulatory photoperiod genes, Ppd-A and Ppd-B and vernalization genes Vrn-A1, and Vrn3. However, these loci explained only 5 to 20% of variance for days to heading. Seven QTLs overlapped between the two germplasm groups in which Q.ICD.Eps-03 and Q.ICD.Vrn-17 consistently affected flowering time in all the pheno-environments, while Q.ICD.Eps-11 and Q.ICD.Ppd-12 were significant only in two pheno-environments and the combined analysis across all environments. These results help clarify the genetic mechanism controlling flowering time in durum wheat and show some clear distinctions to what is known for common wheat (Triticum aestivum L.)

scholarly journals A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation

PLoS Genetics ◽  
2008 ◽  
Vol 4 (5) ◽  
pp. e1000074 ◽  
Author(s):  
Jiali Han ◽  
Peter Kraft ◽  
Hongmei Nan ◽  
Qun Guo ◽  
Constance Chen ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Skin Pigmentation ◽  
Genome Wide Association ◽  
Hair Color ◽  
Genome Wide ◽  
A Genome ◽  
Novel Alleles

Identification of Earliness Per Se Flowering Time Locus in Spring Wheat through a Genome-Wide Association Study

Crop Science ◽  
2016 ◽  
Vol 56 (6) ◽  
pp. 2962-2672 ◽  
Author(s):  
Sivakumar Sukumaran ◽  
Marta S. Lopes ◽  
Susanne Dreisigacker ◽  
Laura E. Dixon ◽  
Meluleki Zikhali ◽  
...  
Keyword(s):  
Association Study ◽  
Flowering Time ◽  
Spring Wheat ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Earliness Per Se ◽  
Genome Wide ◽  
A Genome ◽  
Per Se

scholarly journals Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259690
Author(s):  
Paula Díaz ◽  
Felipe Sarmiento ◽  
Boby Mathew ◽  
Agim Ballvora ◽  
Teresa Mosquera Vásquez
Keyword(s):  
Water Deficit ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Tuber Initiation ◽  
Stress Index ◽  
Phenotypic Variance ◽  
Diploid Potato ◽  
Nucleotide Polymorphisms ◽  
A Genome ◽  
Initiation Stage

Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain between 12.6% and 44.1% of the phenotypic variance. A set of 6 QTL were found to be associated with more than one variable. Marker WDP-9.21 was found associated with tuber fresh weigh under WD and gene annotation analysis revealed co-localization with the Glucan/water dikinase (GWD) gene. Of the nine QTL detected from DTI on chromosomes 2,3,5,8,10 and 12, three candidate genes with a feasible role in water deficit response were identified. The findings of this study can be used in marker-assisted selection (MAS) for water- deficit tolerance breeding in potato.

scholarly journals Genomic Regions Associated with the Control of Flowering Time in Durum Wheat

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1628
Author(s):  
Priyanka Gupta ◽  
Hafssa Kabbaj ◽  
Khaoula El Hassouni ◽  
Marco Maccaferri ◽  
Miguel Sanchez-Garcia ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Flowering Time ◽  
Genome Wide Association Study ◽  
Strong Association ◽  
Day Length ◽  
Nucleotide Polymorphisms ◽  
Significant Qtls ◽  
A Genome ◽  
Days To Heading ◽  
Genomic Regions

Flowering time is a critical stage for crop development as it regulates the ability of plants to adapt to an environment. To understand the genetic control of flowering time, a genome-wide association study (GWAS) was conducted to identify the genomic regions associated with the control of this trait in durum wheat (Triticum durum Desf.). A total of 96 landraces and 288 modern lines were evaluated for days to heading, growing degree days, and accumulated day length at flowering across 13 environments spread across Morocco, Lebanon, Mauritania, and Senegal. These environments were grouped into four pheno-environments based on temperature, day length, and other climatic variables. Genotyping with a 35K Axiom array generated 7652 polymorphic single nucleotide polymorphisms (SNPs) in addition to 3 KASP markers associated with known flowering genes. In total, 32 significant QTLs were identified in both landraces and modern lines. Some QTLs had a strong association with already known regulatory photoperiod genes, Ppd-A and Ppd-B, and vernalization genes Vrn-A1 and VrnA7. However, these loci explained only 5% to 20% of variance for days to heading. Seven QTLs overlapped between the two germplasm groups in which Q.ICD.Eps-03 and Q.ICD.Vrn-15 consistently affected flowering time in all the pheno-environments, while Q.ICD.Eps-09 and Q.ICD.Ppd-10 were significant only in two pheno-environments and the combined analysis across all environments. These results help clarify the genetic mechanism controlling flowering time in durum wheat and show some clear distinctions to what is known for common wheat (Triticum aestivum L.).

scholarly journals Genetic Architecture of Flowering Time and Sex Determination in Hemp (Cannabis sativa L.): A Genome-Wide Association Study

2020 ◽  
Vol 11 ◽  
Author(s):  
Jordi Petit ◽  
Elma M. J. Salentijn ◽  
Maria-João Paulo ◽  
Christel Denneboom ◽  
Luisa M. Trindade
Keyword(s):  
Sex Determination ◽  
Association Study ◽  
Flowering Time ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Cannabis Sativa ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Identification of genetic loci and candidate genes related to soybean flowering through genome wide association study

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Minmin Li ◽  
Ying Liu ◽  
Yahan Tao ◽  
Chongjing Xu ◽  
Xin Li ◽  
...  
Keyword(s):  
Association Study ◽  
Flowering Time ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Growth Period ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Genome Wide ◽  
A Genome

Abstract Background As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, we performed a genome-wide association study (GWAS) using a panel of 278 soybean accessions and 34,710 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) higher than 0.04 detected by the specific-locus amplified fragment sequencing (SLAF-seq) with a 6.14-fold average sequencing depth. GWAS was conducted by a compressed mixed linear model (CMLM) involving in both relative kinship and population structure. Results GWAS revealed that 37 significant SNP peaks associated with soybean flowering time or other growth periods related traits including full bloom, beginning pod, full pod, beginning seed, and full seed in two or more environments at -log10(P) > 3.75 or -log10(P) > 4.44 were distributed on 14 chromosomes, including chromosome 1, 2, 3, 5, 6, 9, 11, 12, 13, 14, 15, 17, 18, 19. Fourteen SNPs were novel loci and 23 SNPs were located within known QTLs or 75 kb near the known SNPs. Five candidate genes (Glyma.05G101800, Glyma.11G140100, Glyma.11G142900, Glyma.19G099700, Glyma.19G100900) in a 90 kb genomic region of each side of four significant SNPs (Gm5_27111367, Gm11_10629613, Gm11_10950924, Gm19_34768458) based on the average LD decay were homologs of Arabidopsis flowering time genes of AT5G48385.1, AT3G46510.1, AT5G59780.3, AT1G28050.1, and AT3G26790.1. These genes encoding FRI (FRIGIDA), PUB13 (plant U-box 13), MYB59, CONSTANS, and FUS3 proteins respectively might play important roles in controlling soybean growth periods. Conclusions This study identified putative SNP markers associated with soybean growth period traits, which could be used for the marker-assisted selection of soybean growth period traits. Furthermore, the possible candidate genes involved in the control of soybean flowering time were predicted.

scholarly journals Genome-Wide Association Study to Identify Candidate Loci for Biomass Formation Under Water Deficit in Perennial Ryegrass

2020 ◽  
Vol 11 ◽  
Author(s):  
Kristina Jaškūnė ◽  
Andrius Aleliūnas ◽  
Gražina Statkevičiūtė ◽  
Vilma Kemešytė ◽  
Bruno Studer ◽  
...  
Keyword(s):  
Association Study ◽  
Water Deficit ◽  
Perennial Ryegrass ◽  
Water Deprivation ◽  
Genome Wide Association Study ◽  
Leaf Growth ◽  
Genome Wide Association ◽  
Biomass Formation ◽  
Genome Wide ◽  
A Genome

Global warming is predicted to impact many agricultural areas, which will suffer from reduced water availability. Due to precipitation changes, mild summer droughts are expected to become more frequent, even in temperate regions. For perennial ryegrass (Lolium perenne L.), an important forage grass of the Poaceae family, leaf growth is a crucial factor determining biomass accumulation and hence forage yield. Although leaf elongation has been shown to be temperature-dependent under normal conditions, the genetic regulation of leaf growth under water deficit in perennial ryegrass is poorly understood. Herein, we evaluated the response to water deprivation in a diverse panel of perennial ryegrass genotypes, employing a high-precision phenotyping platform. The study revealed phenotypic variation for growth-related traits and significant (P < 0.05) differences in leaf growth under normal conditions within the subgroups of turf and forage type cultivars. The phenotypic data was combined with genotypic variants identified using genotyping-by-sequencing to conduct a genome-wide association study (GWAS). Using GWAS, we identified DNA polymorphisms significantly associated with leaf growth reduction under water deprivation. These polymorphisms were adjacent to genes predicted to encode for phytochrome B and a MYB41 transcription factor. The result obtained in the present study will increase our understanding on the complex molecular mechanisms involved in plant growth under water deficit. Moreover, the single nucleotide polymorphism (SNP) markers identified will serve as a valuable resource in future breeding programs to select for enhanced biomass formation under mild summer drought conditions.

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