scholarly journals Multi-model genome-wide association and genomic prediction analysis of 16 agronomic, physiological and quality related traits in ICARDA spring wheat

Euphytica ◽  
2021 ◽  
Vol 217 (11) ◽  
Author(s):  
Admas Alemu ◽  
Sufian Suliman ◽  
Adel Hagras ◽  
Sherif Thabet ◽  
Ayed Al-Abdallat ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Spring Wheat ◽  
Genomic Prediction ◽  
Marker Assisted Selection ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Chromosome Arm ◽  
Yield Quality ◽  
Trait Associations

AbstractIdentification and exploration of the genetic architecture of traits related to yield, quality, and drought and heat tolerance is important for yield and quality improvement of wheat through marker-assisted selection. One hundred and ninety-two spring wheat genotypes were tested at two heat-stress locations in Sudan (Wad Medani and Dongula), a drought stress site in Morocco (Marchouch) and a site with high yield potential in Egypt (Sids) in replicated trials during the 2015–2016 and 2016–2017 cropping seasons. A total of 10,577 single nucleotide polymorphism markers identified from the 15 K wheat SNP assay were used in a genome-wide association (GWA) study and genomic prediction for 16 phenotypic traits related to yield, quality and drought and heat tolerance. Significant marker-trait associations were detected across GWAS models for all traits. Most detected marker-trait associations (MTAs) were environment-specific, signifying the presence of high quantitative trait loci-by-environment (QTL x E) interaction. Chromosome arm 5AL had significant multi-model MTAs for grain yield and yield-related traits at the heat-stress locations. Highly significant QTLs were detected on chromosome 2D for waxiness. Homoeologous group 2 and 6 chromosomes were with significant MTAs for grain protein content, gluten content, alveograph strength and Zeleny sedimentation test while chromosome arm 3BL was significant for both Z and W traits. Genomic prediction analysis with ridge regression-best linear unbiased prediction model estimated the breeding values of the studied traits with prediction accuracies ranging from 0.16 for leaf rolling to 0.72 for peduncle length. The identified QTLs could be targeted for marker-assisted selection or further studies aimed at fine mapping and cloning the causative genes and detecting favorable haplotypes with positive effects for agronomic, physiological or quality-related traits.

scholarly journals New loci and neuronal pathways for resilience to heat stress in animals

2021 ◽  
Author(s):  
Evans K. Cheruiyot ◽  
Mekonnen Haile-Mariam ◽  
Benjamin G. Cocks ◽  
Iona M. MacLeod ◽  
Ruidong Xiang ◽  
...  
Keyword(s):  
Heat Stress ◽  
Milk Production ◽  
Heat Tolerance ◽  
Genome Wide Association ◽  
Receptor Interaction ◽  
Sequence Variants ◽  
Neuronal System ◽  
Vertebrate Species ◽  
Genome Wide ◽  
Management Approaches

AbstractClimate change and resilience to warming climates have implications for humans, livestock, and wildlife. The genetic mechanisms that confer thermotolerance to mammals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual’s heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature-humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2, and GRIA4) and neuroactive ligand-receptor interaction functions for heat tolerance (NPFFR2, CALCR, and GHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.Author summaryWhile understanding the genetic basis of heat tolerance is crucial in the context of global warming’s effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. The ability to tolerate heat varies across individuals, with substantial genetic control of this complex trait. Dairy cattle are excellent model in which to find genes associated with individual variations in heat tolerance since they significantly suffer from heat stress due to the metabolic heat of lactation. By genome-wide association studies of more than 29,000 cows with 15 million sequence variants and controlled phenotype measurements, we identify many new loci associated with heat tolerance. The biological functions of these loci are linked to the neuronal system and neuroactive ligand-receptor interaction functions. Also, several putative causal mutations for heat tolerance are at genomic sites that are otherwise evolutionarily conserved across 100 vertebrate species. Overall, our findings provide new insight into the molecular and biological basis of heat tolerance that can help to develop genetic and management approaches to combat heat stress.

Comparison of array‐ and sequencing‐based markers for genome‐wide association mapping and genomic prediction in spring wheat

Crop Science ◽  
2020 ◽  
Vol 60 (1) ◽  
pp. 211-225 ◽  
Author(s):  
Caiyun Liu ◽  
Sivakumar Sukumaran ◽  
Diego Jarquin ◽  
Jose Crossa ◽  
Susanne Dreisigacker ◽  
...  
Keyword(s):  
Association Mapping ◽  
Spring Wheat ◽  
Genomic Prediction ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11857
Author(s):  
Akerke Amalova ◽  
Saule Abugalieva ◽  
Adylkhan Babkenov ◽  
Sandukash Babkenova ◽  
Yerlan Turuspekov
Keyword(s):  
Association Study ◽  
Spring Wheat ◽  
Marker Assisted Selection ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Northern Kazakhstan ◽  
Genome Wide ◽  
Rainfed Conditions ◽  
Selection Approach

Background Bread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach. Methods A collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits. Results Out of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach.

scholarly journals Genome-wide association studies on heat stress tolerance during grain development in wheat (Triticum aestivum L.)

2020 ◽  
Author(s):  
Jie Guo ◽  
Weiping Shi ◽  
Jiahui Guo ◽  
Linqi Yue ◽  
Lei Zhuang ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Association Studies ◽  
Starch Content ◽  
Kernel Weight ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genome Wide Association Studies ◽  
Wheat Cultivars ◽  
Genome Wide

Abstract BackgroundHeat stress at the late reproductive stages is a common problem encountered in autumn-sown wheat production regions in China with the affected area covering as much as two-thirds of the crop. In order to develop wheat cultivars with heat-tolerance, it is crucial to explore favorable alleles for use in breeding programs.ResultsIn this study, we performed a 90K iSelect SNP genotyping assay on a collection of 207 wheat cultivars subjected to heat stress during grain-fill growth stage in three years (2015-2017). Genotypic analyses of 19 phenotypic traits revealed that heat stress had major impacts on grain weight, size, and quality. Correlation analyses indicated that thousand kernel weight (TKW) was significantly correlated with grain width (GW) and grain perimeter (GP), whereas grain protein content (GPC) was negatively correlated with total starch content (TSC) (P <0.01). We applied heat susceptibility indices (HSI) for different traits to assess heat tolerance. Genome-wide association studies (GWAS) revealed a total of 125 marker-trait associations (MTAs) at 63 SNP loci on 16 chromosomes each accounting for phenotypic variation (R2) of 3.0-21.4%. 17 loci showed significant associations in three environments. The analysis of selective sweeps indicated that RAC875_c19042_2102 (2B), wsnp_Ex_c257_491667 (3B), wsnp_Ex_rep_c101323_86702413 (5A) and BS00061911_51 (7A) were selected between two subpopulations (top 5%).ConclusionsThese four key MTAs detected in the present study are candidates for further genetic dissection and development of molecular markers.

scholarly journals Genome-wide association study of leaf rust resistance in Russian spring wheat varieties

2020 ◽  
Vol 20 (S1) ◽  
Author(s):  
Irina N. Leonova ◽  
Ekaterina S. Skolotneva ◽  
Elena A. Salina
Keyword(s):  
Association Study ◽  
Leaf Rust ◽  
Spring Wheat ◽  
Marker Assisted Selection ◽  
Rust Resistance ◽  
Genome Wide Association Study ◽  
Leaf Rust Resistance ◽  
Genome Wide Association ◽  
Wheat Varieties ◽  
Genome Wide

Abstract Background Leaf rust (Puccinia triticina Eriks.) is one of the most dangerous diseases of common wheat worldwide. Three approaches: genome-wide association study (GWAS), marker-assisted selection (MAS) and phytopathological evaluation in field, were used for assessment of the genetic diversity of Russian spring wheat varieties on leaf rust resistance loci and for identification of associated molecular markers. Results The collection, consisting of 100 Russian varieties of spring wheat, was evaluated over three seasons for resistance to the native population of leaf rust specific to the West Siberian region of Russia. The results indicated that most cultivars showed high susceptibility to P. triticina, with severity ratings (SR) of 60S–90S, however some cultivars showed a high level of leaf rust resistance (SR < 20MR-R). Based on the results of genome-wide association studies (GWAS) performed using the wheat 15 K genotyping array, 20 SNPs located on chromosomes 6D, 6A, 6B, 5A, 1B, 2A, 2B and 7A were revealed to be associated with leaf rust resistance. Genotyping with markers developed for known leaf rust resistance genes showed that most of the varieties contain genes Lr1, Lr3a, Lr9, Lr10, Lr17a, Lr20, Lr26 and Lr34, which are not currently effective against the pathogen. In the genome of three wheat varieties, gene Lr6Ai = 2 inherited from Th. intermedium was detected, which provides complete protection against the rust pathogen. It has been suggested that the QTL mapped to the chromosome 5AS of wheat cultivar Tulaikovskaya-zolotistaya, Tulaikovskaya-10, Samsar, and Volgouralskaya may be a new, previously undescribed locus conferring resistance to leaf rust. Obtained results also indicate that chromosome 1BL of the varieties Sonata, Otrada-Sibiri, Tertsiya, Omskaya-23, Tulaikovskaya-1, Obskaya-14, and Sirena may contain an unknown locus that provides a resistance response to local population. Conclusions This study provides new insights into the genetic basis of resistance to leaf rust in Russian spring wheat varieties. The SNPs significantly associated with leaf rust resistance can be used for the development and application of diagnostic markers in marker-assisted selection schemes.

scholarly journals Genome wide association mapping for heat tolerance in sub-tropical maize

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ningthaipuilu Longmei ◽  
Gurjit Kaur Gill ◽  
Pervez Haider Zaidi ◽  
Ramesh Kumar ◽  
Sudha Krishnan Nair ◽  
...  
Keyword(s):  
Heat Stress ◽  
Association Mapping ◽  
Heat Tolerance ◽  
Stress Conditions ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Multiple Traits ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Heat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollination failure and barren ears that causes devastating yield losses. So, there is need to identify the genomic regions associated with heat tolerance component traits which could be further employed in maize breeding program. Results An association mapping panel, consisting of 662 doubled haploid (DH) lines, was evaluated for yield contributing traits under normal and natural heat stress conditions. Genome wide association studies (GWAS) carried out using 187,000 SNPs and 130 SNPs significantly associated for grain yield (GY), days to 50% anthesis (AD), days to 50% silking (SD), anthesis-silking interval (ASI), plant height (PH), ear height (EH) and ear position (EPO) were identified under normal conditions. A total of 46 SNPs strongly associated with GY, ASI, EH and EPO were detected under heat stress conditions. Fifteen of the SNPs was found to have common association with more than one trait such as two SNPs viz. S10_1,905,273 and S10_1,905,274 showed colocalization with GY, PH and EH whereas S10_7,132,845 SNP associated with GY, AD and SD under normal conditions. No such colocalization of SNP markers with multiple traits was observed under heat stress conditions. Haplotypes trend regression analysis revealed 122 and 85 haplotype blocks, out of which, 20 and 6 haplotype blocks were associated with more than one trait under normal and heat stress conditions, respectively. Based on SNP association and haplotype mapping, nine and seven candidate genes were identified respectively, which belongs to different gene models having different biological functions in stress biology. Conclusions The present study identified significant SNPs and haplotype blocks associated with yield contributing traits that help in selection of donor lines with favorable alleles for multiple traits. These results provided insights of genetics of heat stress tolerance. The genomic regions detected in the present study need further validation before being applied in the breeding pipelines.

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