scholarly journals Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Hu ◽  
Changmian Ji ◽  
Zhe Liang ◽  
Jianqiu Ye ◽  
Wenjun Ou ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Allelic Variation ◽  
Starch Content ◽  
Genomic Variation ◽  
Root Weight ◽  
Storage Root ◽  
Cassava Bacterial Blight ◽  
A Genome ◽  
Selection For

Abstract Background Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome. Results We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB. Conclusions This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.

scholarly journals A genome-wide association study unravels cytokinin as a major component in the root defense responses against Ralstonia solanacearum

2021 ◽  
Author(s):  
Alejandro Alonso-Díaz ◽  
Santosh B Satbhai ◽  
Roger de Pedro-Jové ◽  
Hannah M Berry ◽  
Christian Göschl ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Defense Responses ◽  
Genome Wide Association ◽  
Root Growth Inhibition ◽  
Future Research ◽  
Cytokinin Signaling ◽  
Genome Wide ◽  
A Genome

Abstract Bacterial wilt caused by the soil-borne pathogen Ralstonia solancearum is economically devastating, with no effective methods to fight the disease. This pathogen invades plants through their roots and colonizes their xylem, clogging the vasculature and causing rapid wilting. Key to preventing colonization are the early defense responses triggered in the host’s root upon infection, which remain mostly unknown. Here, we have taken advantage of a high-throughput in vitro infection system to screen natural variability associated to the root growth inhibition phenotype caused by R. solanacearum in Arabidopsis during the first hours of infection. To analyze the genetic determinants of this trait, we have performed a Genome-Wide Association Study, identifying allelic variation at several loci related to cytokinin metabolism, including genes responsible for biosynthesis and degradation of cytokinin. Further, our data clearly demonstrate that cytokinin signaling is induced early during the infection process and cytokinin contributes to immunity against R. solanacearum. This study highlights a new role of cytokinin in root immunity, paving the way for future research that will help understanding the mechanisms underpinning root defenses.

scholarly journals Genomic variation across a clinical Cryptococcus population linked to disease outcome

2021 ◽  
Author(s):  
Poppy Channa Sakti Sephton-Clark ◽  
Jennifer Tenor ◽  
Dena Toffaletti ◽  
Nancy Meyers ◽  
Charles Giamberardino ◽  
...  
Keyword(s):  
Patient Outcomes ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Sugar Transport ◽  
Genomic Variation ◽  
Clinical Isolates ◽  
Genome Wide ◽  
A Genome ◽  
Gwas Approach

Cryptococcus neoformans is the causative agent of cryptococcosis, a disease with poor patient outcomes, accounting for approximately 180,000 deaths each year. Patient outcomes may be impacted by the underlying genetics of the infecting isolate, however, our current understanding of how genetic diversity contributes to clinical outcomes is limited. Here, we leverage clinical, in vitro growth and genomic data for 284 C. neoformans isolates to identify clinically relevant pathogen variants within a population of clinical isolates from patients with HIV-associated cryptococcosis in Malawi. Through a genome-wide association study (GWAS) approach, we identify variants associated with fungal burden and growth rate. We also find both small and large-scale variation, including aneuploidy, associated with alternate growth phenotypes, which may impact the course of infection. Genes impacted by these variants are involved in transcriptional regulation, signal transduction, glycolysis, sugar transport, and glycosylation. When combined with clinical data, we show that growth within the CNS is reliant upon glycolysis in an animal model, and likely impacts patient mortality, as CNS burden modulates patient outcome. Additionally, we find genes with roles in sugar transport are under selection in the majority of these clinical isolates. Further, we demonstrate that two hypothetical proteins identified by GWAS impact virulence in animal models. Our approach illustrates links between genetic variation and clinically relevant phenotypes, shedding light on survival mechanisms within the CNS and pathways involved in this persistence.

scholarly journals Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Xu ◽  
Di Wu ◽  
Tianquan Yang ◽  
Chao Sun ◽  
Zaiqing Wang ◽  
...  
Keyword(s):  
Castor Bean ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
De Novo ◽  
Agronomic Traits ◽  
Ricinus Communis ◽  
Oilseed Crop ◽  
A Genome ◽  
Trait Locus ◽  
Wild Progenitors

Abstract Background Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean. Results Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size. Conclusions This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.

scholarly journals Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Tilahun Mekonnen ◽  
Clay H. Sneller ◽  
Teklehaimanot Haileselassie ◽  
Cathrine Ziyomo ◽  
Bekele G. Abeyo ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Defense Responses ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Adult Plant ◽  
Putative Qtls ◽  
Association Panel ◽  
A Genome ◽  
Trait Associations

Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26–105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7–13.2% of the total phenotypic variation. Seven of the QTLs (R2 = 2.7–10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.

scholarly journals Identification of Genes Targeted in South African Merino and Afrino Sheep Populations Under Long-Term Selection for Reproduction and Body Weight

2020 ◽  
Author(s):  
Margaretha Snyman ◽  
Sunika Süllwald ◽  
Willem Olivier ◽  
Carina Visser
Keyword(s):  
Body Weight ◽  
South African ◽  
Reproductive Performance ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Reproductive Traits ◽  
Term Selection ◽  
A Genome ◽  
Selection For

Abstract Background: Reproductive performance and body weight are of the utmost economic importance in determining the efficiency of sheep production. Simultaneous selection for increased reproductive performance and early growth traits is a common strategy in many flocks, but ambiguous results regarding the relationship between reproduction and body weight have been reported. The objective of this study was to perform a genome-wide association study (GWAS) in two South African Merino flocks and an Afrino sheep flock that were selected for both reproduction and body weight over decades. The GWAS aimed to identify SNPs associated with genes affecting the traits number of lambs born (NLB), number of lambs weaned (NLW), total weight of lamb weaned (TWW) and body weight (BW) and thus to ascertain which genes were targeted through directional selection.Results: In the GWAS, 16 SNP markers associated with reproductive traits were identified among the three populations, while 15 SNPs were associated with body weight. These SNPs were linked respectively to 26 and 21 documented genes in the sheep genome. Most of these genes were previously associated in literature with reproduction related, as well as with growth related traits in various farm animal species. This study, supported by results from previous studies performed on sheep and cattle, identified the following genes that warrant further investigation as to their functions and processes relating to growth and reproduction in sheep: MAP7D1, TRAPPC3, THRAP3, TRMP8, SPP2, HDAC9, ZFHX3, SIX6, C14orf39, TAF4B, TRSP1 EYA2, RBMS3, STL38L, BSPH1, LIG1, CABP5 and ELSPBP1. Conclusions: Long-term selection in the flocks for both body weight and reproductive traits, and especially on the composite trait TWW, have favoured genes with pleiotropic effects influencing both groups of traits. SNPs associated with these pleiotropic genes were detected in the association analyses for the various traits.

scholarly journals Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
João Vitor Maldonado dos Santos ◽  
Everton Geraldo Capote Ferreira ◽  
André Luiz de Lima Passianotto ◽  
Bruna Bley Brumer ◽  
Adriana Brombini Dos Santos ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Major Gene ◽  
Cost Effective ◽  
Stem Canker ◽  
Snp Marker ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
A Genome ◽  
Marker Assay

Abstract Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. Results We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. Conclusions Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.

scholarly journals Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

2020 ◽  
Vol 21 (12) ◽  
pp. 4263
Author(s):  
Alicja Macko-Podgórni ◽  
Katarzyna Stelmach ◽  
Kornelia Kwolek ◽  
Gabriela Machaj ◽  
Shelby Ellison ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Expression Profiles ◽  
Secondary Growth ◽  
Chromosome 1 ◽  
Phenotypic Variance ◽  
Storage Root ◽  
A Genome ◽  
Elevated Expression ◽  
Edible Roots ◽  
Diverse Groups

Background: Diverse groups of carrot cultivars have been developed to meet consumer demands and industry needs. Varietal groups of the cultivated carrot are defined based on the shape of roots. However, little is known about the genetic basis of root shape determination. Methods: Here, we used 307 carrot plants from 103 open-pollinated cultivars for a genome wide association study to identify genomic regions associated with the storage root morphology. Results: A 180 kb-long region on carrot chromosome 1 explained 10% of the total observed phenotypic variance in the shoulder diameter. Within that region, DcDCAF1 and DcBTAF1 genes were proposed as candidates controlling secondary growth of the carrot storage root. Their expression profiles differed between the cultivated and the wild carrots, likely indicating that their elevated expression was required for the development of edible roots. They also showed higher expression at the secondary root growth stage in cultivars producing thick roots, as compared to those developing thin roots. Conclusions: We provided evidence for a likely involvement of DcDCAF1 and/or DcBTAF1 in the development of the carrot storage root and developed a genotyping assay facilitating the identification of variants in the region on carrot chromosome 1 associated with secondary growth of the carrot root.

scholarly journals opulation Structure Analysis and Genome-Wide Association Study of Rice Landraces from Qiandongnan, China, using Specific–Locus Amplified Fragment Sequencing

2021 ◽  
Vol 25 (02) ◽  
pp. 388-396
Author(s):  
Yan Li
Keyword(s):  
Association Study ◽  
Complex Traits ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Genome Wide Association ◽  
Rice Landraces ◽  
Genome Wide ◽  
Sequencing Method ◽  
A Genome ◽  
Specific Locus

Uncovering the genetic basis of rice landraces has important applications in breeding. In this study, the specific-locus amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) of the agronomic traits of 60 rice species in Southeast Guizhou. We obtained a total of 178,287,776 reads, 314,065 SLAFs, and 571,521 single nucleotide polymorphisms (SNPs). A neighbor-joining phylogenetic tree, admixture proportions, and principal component analyses revealed that the investigated landraces were divided into japonica (heterozygosity rate 0.062) and indica (heterozygosity rate 0.073) groups. The groupings were consistent with the local classifications of ―He‖ and ―Gu‖ based on the resistance to seed shattering, and the SNPs clustered in the qSH1 gene. The GWAS of eight agronomic traits revealed that the signal peaks at four locations were closely related to previously reported genes or gene regions. This study demonstrates that the SLAF sequencing method combined with a GWAS may be effective for investigating the evolution of rice and identifying genes regulating complex traits in rice landraces cultivated in relatively isolated regions. © 2021 Friends Science Publishers

scholarly journals Genome-wide association mapping for agronomic and quality traits in foxtail millet

2019 ◽  
Author(s):  
Yanhong Lou ◽  
Yun Chen ◽  
Zhihao Liu ◽  
Mingjie Sun ◽  
Fei Han ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Foxtail Millet ◽  
Significant Snps ◽  
Genomic Variation ◽  
Genome Wide Association ◽  
Quality Traits ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genome Wide ◽  
A Genome

Abstract Background: Foxtail millet [Setaria italica (L.) P. Beauv.] is a particularly important cereal and fodder crop in arid and semi-arid regions. The genomic variation and alleles underpinning agronomic and quality traits are important for foxtail millet improvement. To better understand the diversity of foxtail millet and facilitate the genetic dissection of its agronomic and quality traits, we used high-quality single nucleotide polymorphisms (SNPs) to perform a genome-wide association study (GWAS). Results: Using genotyping-by-sequencing, 107 foxtail millet accessions were sequenced, and further analysis revealed 72,181 high-quality SNPs, of which 53 were significantly associated with 15 agronomic and quality traits. These SNPs were distributed across the nine chromosomes of foxtail millet; 44 were located in intergenic regions, whereas one and eight SNPs were located in exon and intron regions, respectively. The GWAS revealed that 28 SNPs were associated with a single trait. Conclusions: For some of the significant SNPs, favourable genotypes showed pyramiding effects for several traits. The 53 loci identified in this study will therefore be useful for breeding programs aimed at foxtail millet improvement.

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