scholarly journals Molecular Markers Associated with Agro-Physiological Traits under Terminal Drought Conditions in Bread Wheat

2020 ◽  
Vol 21 (9) ◽  
pp. 3156 ◽  
Author(s):  
Sajid Shokat ◽  
Deepmala Sehgal ◽  
Prashant Vikram ◽  
Fulai Liu ◽  
Sukhwinder Singh
Keyword(s):  
Drought Stress ◽  
Genome Wide Association Study ◽  
Genomic Analysis ◽  
Kernel Weight ◽  
Physiological Traits ◽  
Breeding Lines ◽  
Terminal Stage ◽  
Terminal Drought ◽  
Genome Wide ◽  
Population Structure Analysis

Terminal drought stress poses a big challenge to sustain wheat grain production in rain-fed environments. This study aimed to utilize the genetically diverse pre-breeding lines for identification of genomic regions associated with agro-physiological traits at terminal stage drought stress in wheat. A total of 339 pre-breeding lines panel derived from three-way crosses of ‘exotics × elite × elite’ lines were evaluated in field conditions at Obregon, Mexico for two years under well irrigated as well as drought stress environments. Drought stress was imposed at flowering by skipping the irrigations at pre and post anthesis stage. Results revealed that drought significantly reduced grain yield (Y), spike length (SL), number of grains spikes−1 (NGS) and thousand kernel weight (TKW), while kernel abortion (KA) was increased. Population structure analysis in this panel uncovered three sub-populations. Genome wide linkage disequilibrium (LD) decay was observed at 2.5 centimorgan (cM). The haplotypes-based genome wide association study (GWAS) identified significant associations of Y, SL, and TKW on three chromosomes; 4A (HB10.7), 2D (HB6.10) and 3B (HB8.12), respectively. Likewise, associations on chromosomes 6B (HB17.1) and 3A (HB7.11) were found for NGS while on chromosome 3A (HB7.12) for KA. The genomic analysis information generated in the study can be efficiently utilized to improve Y and/or related parameters under terminal stage drought stress through marker-assisted breeding.

scholarly journals GWAS Analysis of Wheat Pre-breeding Germplasm for Terminal Drought Stress Using Next Generation Sequencing Technology

2020 ◽  
Author(s):  
Sajid Shokat ◽  
Deepmala Sehgal ◽  
Fulai Liu ◽  
Sukhwinder Singh
Keyword(s):  
Drought Stress ◽  
Candidate Genes ◽  
Vegetation Index ◽  
Genome Wide Association Study ◽  
Potential Candidate ◽  
Terminal Drought ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
A Genome ◽  
Terminal Drought Stress

Bread wheat (Triticum aestivum L.) is one of the most important cereal crops for food security. Of all the stresses that curtail wheat productivity, drought has the most detrimental effects. Especially terminal drought stress i.e. at the time of flowering imposes a big challenge to sustain grain production. In the current study, 339 pre-breeding lines derived from three-way crosses of exotics x elite lines were evaluated in the irrigated and drought stress environments at Obregon, Mexico for the year 2016 and 2018. Drought significantly reduced yield (Y), spike length (SL), number of grains per spikes (NGS) and thousand kernel weight (TKW) by 46.4, 19.2, 23.5 and 25.9%, respectively in comparison to irrigated conditions. Kernel abortion (KA), highly correlated with Y, increased significantly (11.6%) under drought stress environment. Population structure analysis in this panel revealed three sub-populations and a genome wide linkage disequilibrium (LD) decay was at 2.5 cM. Single marker and haplotypes-based genome wide association study (GWAS) revealed significant associations on three chromosomes; 4A (HB10.7), 2D (HB6.10) and 3B (HB8.12) with Y, SL and TKW, respectively. Likewise, associations on chromosomes 6B (HB17.1) and 3A (HB7.11) were identified for NGS and on 3A (HB7.12) for KA. Five traits i.e. normalized difference vegetation index (NDVI), canopy temperature depression (CTD) days to heading (DTH), NGS, KA were associated at chromosome 3A both under irrigated and drought conditions however, different haplotypes were estimated. Twenty-six SNPs were part of 10 haplotype blocks associated with Y, SL, TKW, NGS and KA. In silico analysis of the associated SNPs/haplotypes showed hits with candidate genes known to confer abiotic stress resistance in model species and crops. Potential candidate genes include those coding for sulfite exporter TauE/SafE family in Arabidopsis thaliana, TBC domain containing protein in Oryza sativa subsp. Japonica and heat shock proteins in Aegilops tauschii subsp. tauschii were revealed. The SNPs linked to the promising genes identified in the study can be used for marker-assisted selection.

scholarly journals Genome-Wide Association Mapping of Late Blight Tolerance Trait in Potato (Solanum tuberosum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Fang Wang ◽  
Meiling Zou ◽  
Long Zhao ◽  
Zhiqiang Xia ◽  
Jian Wang
Keyword(s):  
Solanum Tuberosum ◽  
Late Blight ◽  
Potato Breeding ◽  
Genome Wide Association Study ◽  
Solanum Tuberosum L ◽  
Potato Cultivars ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
A Genome

Uncovering the genetic basis and optimizing the late blight tolerance trait in potatoes (Solanum tuberosum L.) are crucial for potato breeding. Late blight disease is one of the most significant diseases hindering potato production. The traits of late blight tolerance were evaluated for 284 potato cultivars to identify loci significantly associated with the late blight tolerance trait. Of all, 37 and 15 were the most tolerant to disease, and 107 and 30 were the most susceptible. A total of 22,489 high-quality single-nucleotide polymorphisms and indels were identified in 284 potato cultivars. All the potato cultivars were clustered into eight subgroups using population structure analysis and principal component analysis, which were consistent with the results of the phylogenetic tree analysis. The average genetic diversity for all 284 potato cultivars was 0.216, and the differentiation index of each subgroup was 0.025–0.149. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about 0.9 kb. A genome-wide association study using a mixed linear model identified 964 loci significantly associated with the late blight tolerance trait. Fourteen candidate genes for late blight tolerance traits were identified, including genes encoding late blight tolerance protein, chitinase 1, cytosolic nucleotide-binding site–leucine-rich repeat tolerance protein, protein kinase, ethylene-responsive transcription factor, and other potential plant tolerance-related proteins. This study provides novel insights into the genetic architecture of late blight tolerance traits and will be helpful for late blight tolerance in potato breeding.

scholarly journals Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mahesh Pujar ◽  
S. Gangaprasad ◽  
Mahalingam Govindaraj ◽  
Sunil S. Gangurde ◽  
A. Kanatti ◽  
...  
Keyword(s):  
Association Study ◽  
Protein Content ◽  
Pearl Millet ◽  
Genome Wide Association Study ◽  
Breeding Strategy ◽  
Genome Wide Association ◽  
Late Embryogenesis Abundant Protein ◽  
Pentatricopeptide Repeat ◽  
Genome Wide ◽  
Population Structure Analysis

Abstract Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.

Genome-wide association study for agronomic and physiological traits in spring wheat evaluated in a range of heat prone environments

2017 ◽  
Vol 130 (9) ◽  
pp. 1819-1835 ◽  
Author(s):  
Francis C. Ogbonnaya ◽  
Awais Rasheed ◽  
Emeka C. Okechukwu ◽  
Abdulqader Jighly ◽  
Farid Makdis ◽  
...  
Keyword(s):  
Association Study ◽  
Spring Wheat ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Physiological Traits ◽  
Genome Wide

scholarly journals Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning

2020 ◽  
Vol 8 (12) ◽  
pp. 2043
Author(s):  
Shawn M. Higdon ◽  
Bihua C. Huang ◽  
Alan B. Bennett ◽  
Bart C. Weimer
Keyword(s):  
Machine Learning ◽  
Nitrogen Fixation ◽  
Genome Wide Association Study ◽  
Population Genomics ◽  
Genomic Analysis ◽  
Oxidation Reduction ◽  
Genome Wide ◽  
Biological Nitrogen ◽  
Carbohydrate Catabolism ◽  
Comparative Population

Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.

scholarly journals Genome-Wide Association Study of Spot Form of Net Blotch Resistance in the Upper Midwest Barley Breeding Programs

2017 ◽  
Vol 107 (1) ◽  
pp. 100-108 ◽  
Author(s):  
R. R. Burlakoti ◽  
S. Gyawali ◽  
S. Chao ◽  
K. P. Smith ◽  
R. D. Horsley ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
The United States ◽  
Genome Wide Association ◽  
Net Blotch ◽  
Upper Midwest ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Barley Breeding ◽  
Genome Wide

Pyrenophora teres f. maculata, the causal agent of spot form of net blotch (SFNB), is an emerging pathogen of barley in the United States and Australia. Compared with net form of net blotch (NFNB), less is known in the U.S. Upper Midwest barley breeding programs about host resistance and quantitative trait loci (QTL) associated with SFNB in breeding lines. The main objective of this study was to identify QTL associated with SFNB resistance in the Upper Midwest two-rowed and six-rowed barley breeding programs using a genome-wide association study approach. A total of 376 breeding lines of barley were evaluated for SFNB resistance at the seedling stage in the greenhouse in Fargo in 2009. The lines were genotyped with 3,072 single nucleotide polymorphism (SNP) markers. Phenotypic evaluation showed a wide range of variability among populations from the four breeding programs and the two barley-row types. The two-rowed barley lines were more susceptible to SFNB than the six-rowed lines. Continuous distributions of SFNB severity indicate the quantitative nature of SFNB resistance. The mixed linear model (MLM) analysis, which included both population structure and kinship matrices, was used to identify significant SNP-SFNB associations. Principal component analysis was used to control false marker-trait association. The linkage disequilibrium (LD) estimates varied among chromosomes (10 to 20 cM). The MLM analysis identified 10 potential QTL in barley: SFNB-2H-8-10, SFNB-2H-38.03, SFNB-3H-58.64, SFNB-3H-78.53, SFNB-3H-91.88, SFNB-3H-117.1, SFNB-5H-155.3, SFNB-6H-5.4, SFNB-6H-33.74, and SFNB-7H-34.82. Among them, four QTL (SFNB-2H-8-10, SFNB-2H-38.03 SFNB-3H-78.53, and SFNB-3H-117.1) have not previously been published. Identification of SFNB resistant lines and QTL associated with SFNB resistance in this study will be useful in the development of barley genotypes with better SFNB resistance.

scholarly journals Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress

2019 ◽  
Author(s):  
Xueling Ye ◽  
Jian Li ◽  
Yukun Cheng ◽  
Fangjie Yao ◽  
Li Long ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Stripe Rust ◽  
Genome Wide Association Study ◽  
Puccinia Striiformis ◽  
Kernel Weight ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Meristem Development ◽  
The World

Abstract Background As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to multi-environmental yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44059 polymorphic markers from the 55K single nucleotide polymorphism (SNP) chip. Results A total of 13 stable quantitative trait loci (QTLs) were found to be highly associating to yield-related traits, including 6 for spike length (SL), 3 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 2 for both TKW and KWPS, in at least two test environments under stripe rust stress conditions. Of them, ten QTLs were overlapped or very close to the reported QTLs, three QTLs, QSL.sicau-1AL, QTKW.sicau-4AL, and QKWPS.sicau-4AL.1, were potentially novel through the physical location comparison with previous QTLs. Further, twenty-one candidate genes within three potentially novel QTLs were identified, they were mainly involved in the regulation of phytohormone, cell division and proliferation, meristem development, plant or organ development, and carbohydrate transport. Conclusions QTLs and candidate genes detected in our study for yield-related traits under stripe rust stress will facilitate elucidating genetic basis of yield-related trait and could be used in marker-assisted selection in wheat yield breeding.

scholarly journals Genome-wide association study of rice rooting ability at the seedling stage

2020 ◽  
Author(s):  
Xin Xu ◽  
Junhua Ye ◽  
Yingying Yang ◽  
Mengchen Zhang ◽  
Qun Xu ◽  
...  
Keyword(s):  
Association Study ◽  
Root Length ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Root Number ◽  
Expression Levels ◽  
Rooting Ability ◽  
Genome Wide ◽  
Population Structure Analysis

Abstract BackgroundRice rooting ability is a complex agronomical trait that displays heterosis and plays an important role in rice growth and production. Only a few quantitative trait loci (QTLs) have been identified by bi-parental population. More genes or QTLs are required to dissect the genetic architecture of rice rooting ability.ResultsTo characterize the genetic basis for rice rooting ability, we used a natural rice population, genotyped by a 90K single nucleotide polymorphism (SNP) array, to identify the loci associated with rooting-related traits through the genome-wide association study (GWAS). Population structure analysis divided the natural population into two subgroups: indica and japonica. We measured four traits for evaluating rice rooting ability, namely root growth ability (RGA), maximum root length (MRL), root length (RL), and root number (RN). Using the association study in three panels consisting of one for the full population, one for indica, and one for japonica, 24 SNPs associated with rooting ability-related traits were identified. Through comparison of the relative expression levels and DNA sequences between germplasm with extreme phenotypes, results showed that LOC_Os05g11810 had non-synonymous variations at the coding region, which may cause differences in root number, and that the expression levels of LOC_Os04g09900 and LOC_Os04g10060 are closely associated with root length variation.ConclusionsThrough evaluation of the rice rooting ability-related traits and the association mapping, we provided useful information for understanding the genetic basis of rice rooting ability and also identified some candidate genes and molecular markers for rice root breeding.

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