Single‐marker and haplotype‐based association analysis of anthracnose ( Colletotrichum dematium) resistance in spinach ( Spinacia oleracea )

2019 ◽  
Vol 139 (2) ◽  
pp. 402-418
Author(s):  
Henry O. Awika ◽  
Kimberly Cochran ◽  
Vijay Joshi ◽  
Renesh Bedre ◽  
Kranthi K. Mandadi ◽  
...  
Keyword(s):  
Association Analysis ◽  
Spinacia Oleracea ◽  
Colletotrichum Dematium ◽  
Single Marker

scholarly journals High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gehendra Bhattarai ◽  
Wei Yang ◽  
Ainong Shi ◽  
Chunda Feng ◽  
Braham Dhillon ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Downy Mildew ◽  
Association Analysis ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Significant Snps ◽  
Snp Markers ◽  
Resistance Locus ◽  
Downy Mildew Resistance ◽  
Mildew Resistance

Abstract Background Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

scholarly journals Population Structure and Association Analysis of Bolting, Plant Height, and Leaf Erectness in Spinach

HortScience ◽  
2016 ◽  
Vol 51 (5) ◽  
pp. 481-486 ◽  
Author(s):  
Jessica Chitwood ◽  
Ainong Shi ◽  
Beiquan Mou ◽  
Michael Evans ◽  
John Clark ◽  
...  
Keyword(s):  
Linear Model ◽  
Plant Height ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Mixed Linear Model ◽  
Snp Markers ◽  
Structured Populations ◽  
United States Department ◽  
Nucleotide Polymorphisms ◽  
Single Marker

Spinach (Spinacia oleracea L.) is an important vegetable worldwide with high nutritional and health-promoting compounds. Bolting is an important trait to consider to grow spinach in different seasons and regions. Plant height and leaf erectness are important traits for machine harvesting. Breeding slow bolting, taller, and more erect spinach cultivars is needed for improved spinach production. A total of 288 United States Department of Agriculture (USDA) spinach accessions were used as the association panel in this research. Single-nucleotide polymorphisms (SNPs) discovered through genotyping by sequencing (GBS) were used for genotyping. Two structured populations and the admixtures were inferred for the 288 spinach accession panel using STRUCTURE and MEGA. Association mapping was conducted using single-marker regression (SMR) in QGene, and general linear model (GLM) and mixed linear model (MLM) built in TASSEL. Three SNP markers, AYZV02001321_398, AYZV02041012_1060, and AYZV02118171_95 were identified to be associated with bolting. Eight SNP markers, AYZV02014270_540, AYZV02250508_2162, AYZV02091523_19842, AYZV02141794_376, AYZV02077023_64, AYZV02210662_2532, AYZV02153224_2197, and AYZV02003975_248 were found to be associated with plant height. Four SNP markers, AYZV02188832_229, AYZV02219088_79, AYZV02030116_256, and AYZV02129827_197 were associated with erectness. These SNP markers may provide breeders with a tool in spinach molecular breeding to select spinach bolting, plant height, and erectness through marker-assisted selection (MAS).

scholarly journals Genetic diversity and association analysis of leafminer (Liriomyza langei) resistance in spinach (Spinacia oleracea)

Genome ◽  
2016 ◽  
Vol 59 (8) ◽  
pp. 581-588 ◽  
Author(s):  
Ainong Shi ◽  
Beiquan Mou
Keyword(s):  
Association Analysis ◽  
Spinacia Oleracea ◽  
Insect Pest ◽  
Genetic Resistance ◽  
Genotyping By Sequencing ◽  
Complex Trait ◽  
Snp Markers ◽  
Minor Effect ◽  
Single Nucleotide ◽  
Wide Range

Leafminer (Liriomyza langei) is a major insect pest of many important agricultural crops, including spinach (Spinacia oleracea). Use of genetic resistance is an efficient, economic, and environment-friendly method to control this pest. The objective of this research was to conduct association analysis and identify single nucleotide polymorphism (SNP) markers associated with leafminer resistance in spinach germplasm. A total of 300 USDA spinach germplasm accessions were used for the association analysis of leafminer resistance. Genotyping by sequencing (GBS) was used for genotyping and 783 SNPs from GBS were used for association analysis. The leafminer resistance showed a near normal distribution with a wide range from 1.1 to 11.7 stings per square centimeter leaf area, suggesting that the leafminer resistance in spinach is a complex trait controlled by multiple genes with minor effect in this spinach panel. Association analysis indicated that five SNP markers, AYZV02040968_7171, AYZV02076752_412, AYZV02098618_4615, AYZV02147304_383, and AYZV02271373_398, were associated with the leafminer resistance with LOD 2.5 or higher. The SNP markers may be useful for breeders to select plants and lines for leafminer resistance in spinach breeding programs through marker-assisted selection.

scholarly journals Marker-trait association analysis for heading and flowering time in wheat by Single Marker Regression

2011 ◽  
Vol 48 (1) ◽  
pp. 113-120
Author(s):  
Dragana Trkulja ◽  
Ankica Kondic-Spika ◽  
Ljiljana Brbaklic ◽  
Borislav Kobiljski
Keyword(s):  
Flowering Time ◽  
Association Analysis ◽  
Trait Association ◽  
Single Marker ◽  
Marker Regression

scholarly journals Single Marker Association Analysis for Unrelated Samples

2017 ◽  
pp. 375-389 ◽  
Author(s):  
Gang Zheng ◽  
Ao Yuan ◽  
Qizhai Li ◽  
Joseph L. Gastwirth
Keyword(s):  
Association Analysis ◽  
Single Marker

scholarly journals Dissection of Allelic Variation Underlying Floral and Fruit Traits in Flare Tree Peony (Paeonia rockii) Using Association Mapping

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Guo ◽  
Chunyan He ◽  
Fangyun Cheng ◽  
Yuan Zhong ◽  
Xinyun Cheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Analysis ◽  
Complex Traits ◽  
Allelic Variation ◽  
Phenotypic Diversity ◽  
Woody Species ◽  
Fruit Traits ◽  
Tree Peony ◽  
Single Marker ◽  
Paeonia Rockii

Allelic variation in floral quantitative traits, including the elements of flowers and fruits, is caused by extremely complex regulatory processes. In the genetic improvement of flare tree peony (Paeonia rockii), a unique ornamental and edible oil woody species in the genus Paeonia, a better understanding of the genetic composition of these complex traits related to flowers and fruits is needed. Therefore, we investigated the genetic diversity and population structure of 160 P. rockii accessions and conducted single-marker association analysis for 19 quantitative flower and fruit traits using 81 EST-SSR markers. The results showed that the population had a high phenotypic diversity (coefficients of variation, 11.87–110.64%) and a high level of genetic diversity (mean number of alleles, NA = 6.09). These accessions were divided into three subgroups by STRUCTURE analysis and a neighbor-joining tree. Furthermore, we also found a low level of linkage disequilibrium between these EST-SSRs and, by single-marker association analysis, identified 134 significant associations, including four flower traits with 11 EST-SSRs and 10 fruit traits with 32 EST-SSRs. Finally, based on the sequence alignment of the associated markers, P280, PS2, PS12, PS27, PS118, PS131, and PS145 may be considered potential loci to increase the yield of flare tree peony. These results laid the foundation for further analysis of the genetic structure of some key traits in P. rockii and had an obvious potential application value in marker-assisted selection breeding.

scholarly journals Correction: Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map

PLoS ONE ◽  
2017 ◽  
Vol 12 (10) ◽  
pp. e0187178
Author(s):  
Amidou N’Diaye ◽  
Jemanesh K. Haile ◽  
Aron T. Cory ◽  
Fran R. Clarke ◽  
John M. Clarke ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Association Analysis ◽  
Wheat Breeding ◽  
High Density ◽  
Consensus Map ◽  
Breeding Lines ◽  
Single Marker
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