Genome-wide association mapping of agronomic traits and carbon isotope discrimination in a worldwide germplasm collection of spring wheat using SNP markers

2015 ◽  
Vol 35 (2) ◽  
Author(s):  
Freddy Mora ◽  
Dalma Castillo ◽  
Bettina Lado ◽  
Ivan Matus ◽  
Jesse Poland ◽  
...  
Keyword(s):  
Association Mapping ◽  
Carbon Isotope ◽  
Spring Wheat ◽  
Carbon Isotope Discrimination ◽  
Agronomic Traits ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Isotope Discrimination ◽  
Genome Wide

Genome-wide association analysis of resistance to Pseudoperonospora cubensis in citron watermelon

Plant Disease ◽  
2021 ◽  
Author(s):  
Dennis Katuuramu ◽  
Sandra Branham ◽  
Amnon Levi ◽  
Patrick Wechter
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Citrullus Lanatus ◽  
Phenotypic Variability ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Pseudoperonospora Cubensis ◽  
Genome Wide ◽  
A Genome

Cultivated sweet watermelon (Citrullus lanatus) is an important vegetable crop for millions of people around the world. There are limited sources of resistance to economically important diseases within C. lanatus, whereas Citrullus amarus has a reservoir of traits that can be exploited to improve C. lanatus for resistance to biotic and abiotic stresses. Cucurbit downy mildew (CDM), caused by Pseudoperonospora cubensis, is an emerging threat to watermelon production. We screened 122 C. amarus accessions for resistance to CDM over two tests (environments). The accessions were genotyped by whole-genome resequencing to generate 2,126,759 single nucleotide polymorphic (SNP) markers. A genome-wide association study was deployed to uncover marker-trait associations and identify candidate genes underlying resistance to CDM. Our results indicate the presence of wide phenotypic variability (1.1 - 57.8%) for leaf area infection, representing a 50.7-fold variation for CDM resistance across the C. amarus germplasm collection. Broad-sense heritability estimate was 0.55, implying the presence of moderate genetic effects for resistance to CDM. The peak SNP markers associated with resistance to P. cubensis were located on chromosomes Ca03, Ca05, Ca07, and Ca11. The significant SNP markers accounted for up to 30% of the phenotypic variation and were associated with promising candidate genes encoding disease resistance proteins, leucine-rich repeat receptor-like protein kinase, and WRKY transcription factor. This information will be useful in understanding the genetic architecture of the P. cubensis-Citrullus spp. patho-system as well as development of resources for genomics-assisted breeding for resistance to CDM in watermelon.

Characterization and genome-wide association mapping of resistance to leaf rust, stem rust and stripe rust in a geographically diverse collection of spring wheat landraces

2017 ◽  
Vol 37 (9) ◽  
Author(s):  
Peace Kankwatsa ◽  
Davinder Singh ◽  
Peter C. Thomson ◽  
Ebrahiem M. Babiker ◽  
John M. Bonman ◽  
...  
Keyword(s):  
Association Mapping ◽  
Leaf Rust ◽  
Stripe Rust ◽  
Spring Wheat ◽  
Stem Rust ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Wheat Landraces

scholarly journals Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

2019 ◽  
Author(s):  
Waltram Ravelombola ◽  
Jun Qin ◽  
Ainong Shi ◽  
Fengmin Wang ◽  
Yan Feng ◽  
...  
Keyword(s):  
Association Study ◽  
Genomic Selection ◽  
Candidate Genes ◽  
Plant Height ◽  
Seed Weight ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Genome Wide

Abstract Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci ( E2 , E4 , and Dt1 ) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent. Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

scholarly journals Genome wide association mapping of agro-morphological traits among a diverse collection of finger millet (Eleusine coracana L.) genotypes using SNP markers

PLoS ONE ◽  
2018 ◽  
Vol 13 (8) ◽  
pp. e0199444 ◽  
Author(s):  
Divya Sharma ◽  
Apoorv Tiwari ◽  
Salej Sood ◽  
Gautam Jamra ◽  
N. K. Singh ◽  
...  
Keyword(s):  
Association Mapping ◽  
Morphological Traits ◽  
Finger Millet ◽  
Snp Markers ◽  
Eleusine Coracana ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome‐Wide Association Mapping of Leaf Rust Response in a Durum Wheat Worldwide Germplasm Collection

2016 ◽  
Vol 9 (3) ◽  
Author(s):  
Meriem Aoun ◽  
Matthew Breiland ◽  
M. Kathryn Turner ◽  
Alexander Loladze ◽  
Shiaoman Chao ◽  
...  
Keyword(s):  
Association Mapping ◽  
Durum Wheat ◽  
Leaf Rust ◽  
Germplasm Collection ◽  
Genome Wide Association ◽  
Genome Wide

Genome-wide association mapping of agronomic traits in relevant barley germplasm in Uruguay

2012 ◽  
Vol 31 (3) ◽  
pp. 631-654 ◽  
Author(s):  
Andrés Locatelli ◽  
Alfonso Cuesta-Marcos ◽  
Lucía Gutiérrez ◽  
Patrick M. Hayes ◽  
Kevin P. Smith ◽  
...  
Keyword(s):  
Association Mapping ◽  
Agronomic Traits ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Barley Germplasm

Genome-wide association mapping of genomic regions associated with phenotypic traits in Canadian western spring wheat

2017 ◽  
Vol 37 (11) ◽  
Author(s):  
Hua Chen ◽  
Kassa Semagn ◽  
Muhammad Iqbal ◽  
Neshat Pazooki Moakhar ◽  
Teketel Haile ◽  
...  
Keyword(s):  
Association Mapping ◽  
Spring Wheat ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genome Wide ◽  
Genomic Regions

Genome-wide association mapping of agronomic traits in sugar beet

2011 ◽  
Vol 123 (7) ◽  
pp. 1121-1131 ◽  
Author(s):  
Tobias Würschum ◽  
Hans Peter Maurer ◽  
Thomas Kraft ◽  
Geert Janssen ◽  
Carolina Nilsson ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Association Mapping ◽  
Agronomic Traits ◽  
Genome Wide Association ◽  
Genome Wide
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