scholarly journals Genome-Wide Association Mapping of Resistance to the Sugarcane Aphid in Sorghum bicolor

2021 ◽  
Author(s):  
Somashekhar Punnuri ◽  
Addissu Ayele ◽  
Karen Harris-Shultz ◽  
Joseph Knoll ◽  
Alisa Coffin ◽  
...  
Keyword(s):  
Flowering Time ◽  
Plant Height ◽  
Genotyping By Sequencing ◽  
Significant Snps ◽  
Aphid Resistance ◽  
Melanaphis Sacchari ◽  
Phenotypic Data ◽  
Sugarcane Aphid ◽  
Genome Wide ◽  
Sorghum Production

Abstract Since 2013, the sugarcane aphid (SCA), Melanaphis sacchari (Zehntner), has been a serious pest that hampers all types of sorghum production in the U.S. Our understanding of sugarcane aphid resistance in sorghum is limited to knowledge about a few genetic regions on chromosome SBI-06. In this study, a subset of the Sorghum Association Panel (SAP) was used along with some additional lines to identify genetic and genomic regions that confer sugarcane aphid resistance. SAP lines were grown in the field and visually evaluated for SCA resistance during the growing seasons of 2019 and 2020 in Tifton, GA. In 2020, the SAP accessions were also evaluated for SCA resistance in the field using drone-based high throughput phenotyping (HTP) and visual scoring under greenhouse conditions. Plant height and flowering time were also recorded in the field to confirm that our methods were sufficient for identifying known quantitative trait loci (QTL). This study combined phenotypic data from field-based visual ratings, reflectance data, and greenhouse evaluations to identify genome-wide associated (GWAS) marker-trait associations (MTA) using genotyping-by-sequencing (GBS) data. Several MTAs were identified for sugarcane aphid-related traits across the genome, with a few common markers that were consistently identified on SBI-08 and SBI-10 for aphid count and plant damage as well as for reflectance indices-based traits on SBI-02, SBI-03, and SBI-05. Candidate genes encoding leucine-rich repeats (LRR), Avr proteins, lipoxygenases (LOXs), calmodulins (CAM) dependent protein kinase, WRKY transcription factors, flavonoid biosynthesis genes, and 12-oxo-phytodienoic acid reductase are identified near SNPs that had significant associations with different SCA traits. In this study, plant height and flowering time-related genes were also identified. The total phenotypic variation explained by significant SNPs across SCA-scored traits, plant height, and flowering time ranged from 0 to 74%, while the heritability value ranged from 4 to 74%. These results supported the existing literature, and also revealed several new loci. Markers identified in this study will support marker-assisted breeding for sugarcane aphid resistance.

scholarly journals Genotyping by sequencing of 393 Sorghum bicolor BTx623 × IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection

2018 ◽  
Author(s):  
WenQian Kong ◽  
Changsoo Kim ◽  
Dong Zhang ◽  
Hui Guo ◽  
Xu Tan ◽  
...  
Keyword(s):  
Flowering Time ◽  
Plant Height ◽  
Recombinant Inbred ◽  
Recombinant Inbred Lines ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Ril Population ◽  
Trait Locus ◽  
Number Of Individuals ◽  
Syntenic Regions

AbstractWe describe a genetic map with a total of 381 bins of 616 genotyping by sequencing (GBS)-based SNP markers in a F6-F8 recombinant inbred line (RIL) population of 393 individuals derived from crossing S. bicolor BTx623 to S. bicolor IS3620C, a guinea line substantially diverged from BTx623. Five segregation distorted regions were found with four showing enrichment for S. bicolor alleles, suggesting possible selection during formation of this RIL population. A quantitative trait locus (QTL) study with this number of individuals, tripled relative to prior studies of this cross, provided resources, validated previous findings, and demonstrated improved power to detect plant height and flowering time related QTLs relative to other published studies. An unexpected low correlation between flowering time and plant height permitted us to separate QTLs for each trait and provide evidence against pleiotropy. Ten non-random syntenic regions conferring QTLs for the same trait suggest that those QTLs may represent alleles at genes functioning in the same manner since the 96 million year ago genome duplication that created these syntenic relationships, while syntenic regions conferring QTLs for different trait may suggest sub-functionalization after duplication. Collectively, this study provides resources for marker-assisted breeding, as well as a framework for fine mapping and subsequent cloning of major genes for important traits such as plant height and flowering time in sorghum.

scholarly journals Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using GWAS

2020 ◽  
Author(s):  
Lingqiang Wang ◽  
Ali Muhammad ◽  
Weicheng Hu ◽  
Jinsheng Yu ◽  
Shahid Ullah Khan ◽  
...  
Keyword(s):  
Plant Height ◽  
Hexaploid Wheat ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Significant Snps ◽  
Leaf Length ◽  
Genome Wide ◽  
A Genome ◽  
Multiple Environments ◽  
Architectural Traits

Abstract Background: Wheat is a staple food crop worldwide. Plant height is a key factor in plant architecture as it plays a crucial role in lodging and thus affects yield and quality. Genome-wide studies are mostly applied in crop plants, due to its advanced genotyping technologies, identification of novel loci, and improved statistical approaches. Results: In this study, the population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by four ML-GWAS and three SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were commonly detected, including seven across multiple environments and thirty-six across multiple methods. Interestingly, five most stable SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, possibly played a role in modulating plant height and flag leaf length. When comparing ML-GWAS methods, pLARmEB was the most powerful and accountable for the detection of 49 significant SNPs that mostly contributed to plant height (36 SNPs). However, in SL-GWAS the FarmCPU model detected most of the significant SNPs. Moreover, a total of 152 candidate genes were found that are likely to be involved in plant growth and development which may provide insightful information related to plant architectural traits.Conclusion: Altogether, our results reveal 174 and 97 significant SNPs controlling plant architectural traits using four ML-GWAS and three SL-GWAS methods, respectively. The detection of the stable loci across multiple environments and methods, possibly play a role in modulating plant architectural traits in hexaploid wheat, and finally will contribute to the discovery of valuable SNP loci for marker-assisted selection (MAS) in wheat molecular breeding.

scholarly journals Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection

2021 ◽  
pp. 1-10
Author(s):  
Karthika Rajendran ◽  
Clarice J. Coyne ◽  
Ping Zheng ◽  
Gopesh Saha ◽  
Dorrie Main ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lens Culinaris ◽  
Agronomic Traits ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Phenotypic Data ◽  
Reference Set ◽  
Genome Wide

Abstract Genotyping of lentil plant genetic resources holds the promise to increase the identification and utilization of useful genetic diversity for crop improvement. The International Center for Agriculture Research in the Dry Areas (ICARDA) lentil reference set plus collection of 176 accessions was genotyped using genotyping-by-sequencing (GBS) and 22,555 SNPs were identified. The population structure was investigated using Bayesian analysis (STRUCTURE, k = 3) and principal component analysis. The two methods are in concordance. Genome-wide association analysis (GWAS) using the filtered SNP set and ICARDA historical phenotypic data discovered putative markers for several agronomic traits including days to first flower, seeds per pod, seed weight and days to maturity. The genetic and genomic resources developed and utilized in this study are available to the research community interested in exploring the ICARDA reference set plus collection using GWAS.

scholarly journals Evaluating Sugarcane Aphid, Melanaphis sacchari (Hemiptera: Aphididae), Population Dynamics, Feeding Injury, and Grain Yield Among Commercial Sorghum Varieties in Alabama

2021 ◽  
Author(s):  
Adrian J Pekarcik ◽  
Alana L Jacobson
Keyword(s):  
Population Dynamics ◽  
Grain Yield ◽  
Abiotic Factors ◽  
Reproductive Potential ◽  
The United States ◽  
Melanaphis Sacchari ◽  
Sugarcane Aphid ◽  
Sorghum Production ◽  
Plant Injury ◽  
Sorghum Bicolor L

Abstract The sugarcane aphid, Melanaphis sacchari (Zehntner), emerged as a severe pest of sorghum, Sorghum bicolor (L.), in Texas and Louisiana in 2013 and currently threatens nearly all sorghum production in the United States. Proper management of populations is critical as sugarcane aphid has a high reproductive potential and can rapidly damage plants, resulting in extensive yield losses. The overall objective of this work was to investigate sugarcane aphid population dynamics, and subsequent sorghum injury and grain yield on commercially available grain sorghum varieties in Alabama. This research includes three-site years of data that show variation in plant injury, physiological maturity, and yields among varieties tested. Although performance of each variety was variable among locations, potentially due to abiotic factors, four varieties including DKS 37-07, 1G588, 1G855, and 83P17 exhibited characteristics consistent with resistance and corroborates reports of resistance from other states.

scholarly journals Associations between gut microbiota and hand grip strength: a polygenetic scoring analysis and genome-wide environmental interaction study

2020 ◽  
Author(s):  
Li Liu ◽  
Bolun Cheng ◽  
Yan Wen ◽  
Yumeng Jia ◽  
Shiqiang Cheng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Grip Strength ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Hand Grip Strength ◽  
Environment Interaction ◽  
Interaction Study ◽  
Phenotypic Data ◽  
Hand Grip ◽  
Genome Wide

Abstract Background We aim to explore the genetic association between hand grip strength (HGS) and gut microbiota (GM). Methods The genome-wide association study (GWAS) data of GM was obtained from a recently published study, involving 2,646 individuals. Phenotypic data of left HGS (n = 375,229) and right HGS (n = 375,279) were derived from the UK Biobank. Firstly, PLINK 2.0 was used to calculate 114 GM related polygenetic risk score (PRS) of each subject based on GWAS result. Regression analysis was then conducted to evaluate the possible association of GM-PRS and HGS. Then genome-wide by environment interaction study (GWEIS) of GM related traits was then performed using a regression model adjusted for age, gender, BMI and 10 principal components. Results For PRS analysis, 13 candidate GM were identified to be associated with left HGS (P < 0.05), including G_Bifidobacterium (P = 8.36 × 10− 4), G_Clostridium_sensu_stricto (P = 2.69 × 10− 3), and 10 significant GM for right HGS, such as G_Acidaminococcus (P = 1.29 × 10− 2), G_Streptococcus (P = 1.79 × 10− 2). In addition, 4 GM were found to be overlapped in association with both left and right HGS, including G_Bifidobacterium (P right HGS = 2.78 × 10− 2, P left HGS = 8.36 × 10− 4). Furthermore, several genome-wide significant GWEIS associations were detected for HGS, including 3 significant SNPs interacted with G_Butyricicoccus (P < 5 × 10− 8) for right HGS (rs41310432, P = 3.86 × 10− 8; closest gene: NASP; rs1053941, P = 4.71 × 10− 8; closest gene: NASP; rs6671239, P = 4.73 × 10− 8, closest gene: GPBP1L1), and 1 suggestive intronic SNP in CACNA1H on chromosome 16 interacted with G_Butyricicoccus (rs139206507, P = 8.68 × 10− 8 ) for left HGS. Conclusions Our study holds great potential gaining a better understanding of the relationship between GM and HGS.

Sign in / Sign up

Export Citation Format

Share Document