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

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.

Download Full-text

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

BMC Genomics ◽

10.1186/s12864-021-07788-8 ◽

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.

Download Full-text

Two SNP Markers Identified Using Genotyping-by-Sequencing Are Associated with Remontancy in a Segregating F1 Population of Syringa meyeri ‘Palibin’ × S. pubescens ‘Penda’ Bloomerang®

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04847-20 ◽

2020 ◽

Vol 145 (2) ◽

pp. 104-109

Author(s):

Hsuan Chen ◽

Jason D. Lattier ◽

Kelly Vining ◽

Ryan N. Contreras

Keyword(s):

Ornamental Plants ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Sequence Information ◽

Specific Marker ◽

Nucleotide Polymorphism ◽

Additive Interaction ◽

Single Nucleotide ◽

Position Information ◽

Flowering Season

Lilacs (Syringa sp.) have been used as ornamental plants since the mid-16th century and remain important in modern gardens due to their attractive and fragrant flowers. However, a short flowering season is a critical drawback for their ornamental value. Breeders have identified remontancy (reblooming) in dwarf lilac (Syringa pubescens), and have tried to introgress this trait into related species by interspecific hybridization. Molecular tools for lilac breeding are limited because of the shortage of genome sequence knowledge and currently no molecular markers are available to use in breeding for remontancy. In this study, an F1 population from crossing Syringa meyeri ‘Palibin’ × S. pubescens ‘Penda’ Bloomerang® Purple was created and subjected to genotyping-by-sequencing (GBS) analysis and phenotyped for remontancy. Plants were categorized as remontant, semi-remontant, and nonremontant based on the relative quantity of inflorescences during the second flush of flowers. A total of 20,730 single-nucleotide polymorphism (SNP) markers from GBS were used in marker-trait association to find remontant-specific marker(s) without marker position information. Two SNP markers, TP70580 (A locus) and TP82604 (B locus), were correlated with remontancy. The two loci showed a partial epistasis and additive interaction effects on the level of remontancy. Accumulation of recessive alleles at the two loci was positively correlated with increased reblooming. For example, 87% of aabb plants were remontant, and only 9% were nonremontant. In contrast, 100% of AaBB plants were nonremontant. These two SNP markers associated with remontancy will be useful in developing markers for future breeding and demonstrate the feasibility of developing markers for breeding woody ornamental taxa that lack a reference genome or extensive DNA sequence information.

Download Full-text

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

HortScience ◽

10.21273/hortsci.51.5.481 ◽

2016 ◽

Vol 51 (5) ◽

pp. 481-486 ◽

Cited By ~ 8

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).

Download Full-text

Genotyping by Multiplexed Sequencing (GMS) protocol in Barley

Euphytica ◽

10.1007/s10681-021-02811-1 ◽

2021 ◽

Vol 217 (4) ◽

Author(s):

Jonathan Eagle ◽

Travis Ruff ◽

Marcus Hooker ◽

Sajal Sthapit ◽

Elliott Marston ◽

...

Keyword(s):

Direct Sequencing ◽

Genotyping By Sequencing ◽

Read Depth ◽

Snp Markers ◽

Direct Sequence ◽

Nucleotide Polymorphism ◽

Accurate Analysis ◽

Single Nucleotide ◽

Analysis Process ◽

Robust Protocol

AbstractGenotyping by sequencing (GBS) and single nucleotide polymorphism (SNP) chip technologies are the primary SNP genotyping technologies used today. However, these genotyping technologies have some drawbacks that limit their usefulness in analysis. We have developed a robust protocol called genotyping by multiplexed sequencing (GMS) using SNP markers, providing informative genotypic data with greater flexibility. The genotypes derived from direct sequence reads reduce ambiguity in genetic analysis. The advantages of this protocol include: (1) This PCR-based direct sequencing protocol generates information from markers of interest and provides a more streamlined and accurate analysis process, by multiplexing hundreds of informative markers into a single sequencing run. (2) The marker sets are easily customized to the species of interest and can readily be changed. In this study we have taken the GMS protocol developed in wheat and adapted it to barley. We have identified 577 SNP markers that work well using this protocol providing adequate genome coverage for genomic selection and tag 267 QTL’s for genes of interest. Good markers have an adequate read depth of at least 5 amplicons and are reliably present across the population.

Download Full-text

Development and Characterization of 37 SNP Markers For The Largemouth Bass (Micropterus Salmoides) By Using PCR-RFLP Method

10.21203/rs.3.rs-472661/v1 ◽

2021 ◽

Author(s):

Zhou Jiang ◽

Jiao Cui ◽

Jiaqi Shao ◽

Chuanju Dong ◽

Jinxing Du ◽

...

Keyword(s):

Largemouth Bass ◽

Polymorphic Information Content ◽

Micropterus Salmoides ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Single Nucleotide ◽

Important Species ◽

Pcr Rflp ◽

Hardy Weinberg Equilibrium

Abstract Largemouth bass (Micropterus salmoides) is an economically important species in China. Contrary to its rapidly increasing yield during the last decades, the domestic genetic diversity of largemouth bass has gradually declined. For further rationally excavation and utilization of largemouth bass germplasm resources, 37 single nucleotide polymorphism (SNP) markers were developed based on genotyping-by-sequencing (GBS) data and characterized by genotyping 32 individuals using the PCR-RFLP method. The effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) of these SNPs ranged from 1.168 to 1.998, 0.156 to 0.844, 0.146 to 0.507, and 0.134 to 0.375, respectively. Totally, five loci deviated significantly from Hardy-Weinberg equilibrium (p < 0.05), while there existed no linkage disequilibrium at all loci. These novel polymorphic markers will lay the foundation for future population and conservation genetics of M. salmoides.

Download Full-text

GWAS identifies a wheat orthologue of the rice D11 gene as an important contributor to grain size in an international collection of hexaploid wheat

10.21203/rs.3.rs-244194/v1 ◽

2021 ◽

Author(s):

Honoré Tekeu ◽

Eddy L.M. Ngonkeu ◽

Sébastien Bélanger ◽

Pierre F. Djocgoué ◽

Amina Abed ◽

...

Keyword(s):

Grain Size ◽

Hexaploid Wheat ◽

Snp Array ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Promising Candidate ◽

Single Nucleotide ◽

Grain Length ◽

Snp Data ◽

Genomic Regions

Abstract Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 159 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-derived genotype calls obtained on Chinese Spring proved extremely accurate when compared to the reference (> 99.9%) and showed > 95% agreement with calls made at SNP loci shared with the 90K SNP array on a subset of 71 Canadian wheat accessions for which both types of data were available. This indicates that GBS can yield a large amount of highly accurate SNP data in hexaploid wheat. The genetic diversity analysis performed using this set of SNP markers revealed the presence of six distinct groups within this collection. A GWAS was conducted to uncover genomic regions controlling variation for grain length and width. In total, seven SNPs were found to be associated with one or both traits, identifying three quantitative trait loci (QTLs) located on chromosomes 1D, 2D and 4A. In the vicinity of the peak SNP on chromosome 2D, we found a promising candidate gene (TraesCS2D01G331100), whose rice ortholog (D11) had previously been reported to be involved in the regulation of grain size. These markers will be useful in breeding for enhanced wheat productivity.

Download Full-text

GWAS identifies an ortholog of the rice D11 gene as a candidate gene for grain size in an international collection of hexaploid wheat

Scientific Reports ◽

10.1038/s41598-021-98626-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Honoré Tekeu ◽

Eddy L. M. Ngonkeu ◽

Sébastien Bélanger ◽

Pierre F. Djocgoué ◽

Amina Abed ◽

...

Keyword(s):

Grain Size ◽

Candidate Gene ◽

Hexaploid Wheat ◽

Snp Array ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Single Nucleotide ◽

Grain Length ◽

Snp Data ◽

Genomic Regions

AbstractGrain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 157 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-derived genotype calls obtained on Chinese Spring proved extremely accurate when compared to the reference (> 99.9%) and showed > 95% agreement with calls made at SNP loci shared with the 90 K SNP array on a subset of 71 Canadian wheat accessions for which both types of data were available. This indicates that GBS can yield a large amount of highly accurate SNP data in hexaploid wheat. The genetic diversity analysis performed using this set of SNP markers revealed the presence of six distinct groups within this collection. A GWAS was conducted to uncover genomic regions controlling variation for grain length and width. In total, seven SNPs were found to be associated with one or both traits, identifying three quantitative trait loci (QTLs) located on chromosomes 1D, 2D and 4A. In the vicinity of the peak SNP on chromosome 2D, we found a promising candidate gene (TraesCS2D01G331100), whose rice ortholog (D11) had previously been reported to be involved in the regulation of grain size. These markers will be useful in breeding for enhanced wheat productivity.

Download Full-text

Marginal Grapevine Germplasm from Apulia (Southern Italy) Represents an Unexplored Source of Genetic Diversity

Agronomy ◽

10.3390/agronomy10040563 ◽

2020 ◽

Vol 10 (4) ◽

pp. 563 ◽

Cited By ~ 1

Author(s):

Monica Marilena Miazzi ◽

Nunzio D’Agostino ◽

Valentina di Rienzo ◽

Pasquale Venerito ◽

Vito Nicola Savino ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Gene Pools ◽

Single Nucleotide ◽

Breeding Programs ◽

Snp Data ◽

Data Points ◽

Genetic Clusters

The investigation on the genetic diversity of grapevine germplasm is crucial for a more efficient use of grapevine genetic resources in light of changing environmental conditions. Here, we used simple sequence repeats (SSRs) coupled with single nucleotide polymorphism (SNP) markers to disclose grapevine genetic diversity of a collection of Apulian minor/neglected genotypes. Their relationships with national or international cultivars were also examined. Genetic diversity was investigated using 10 SSR markers and 1,178 SNPs generated by genotyping by sequencing (GBS). Based on the SSR data, the 128 genotypes were classified into six main genetic clusters. Twenty-four putative cases of synonymy and 2 of misnamings were detected. Ten “unknown” autochthonous genotypes did not show high similarity to Apulian, national, or international varieties. We took advantage of available GBS-derived SNP data points for only forty genotypes to better investigate the genetic distance among them, identify private SNP alleles, and divergent loci putatively under selection. Based on SNP alleles, two interesting gene pools of minor/neglected Apulian samples were identified. Genetic divergence was investigated by FST and allowed the detection of loci capable of differentiating the gene pools. Overall, this work emphasizes the need for recovering the untapped genetic variability that characterizes minor/neglected grapevine Apulian genotypes and the requirement to preserve and use more efficiently grapevine genetic resources in breeding programs.

Download Full-text

Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F5 Population of Pepper with Contrasting Powdery Mildew Resistance Trait

BioMed Research International ◽

10.1155/2021/6673010 ◽

2021 ◽

Vol 2021 ◽

pp. 1-8

Author(s):

Abinaya Manivannan ◽

Sena Choi ◽

Tae-Hwan Jun ◽

Eun-Young Yang ◽

Jin-Hee Kim ◽

...

Keyword(s):

Powdery Mildew ◽

Linkage Map ◽

Powdery Mildew Resistance ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Read Mapping ◽

Single Nucleotide ◽

Mildew Resistance ◽

Polymorphic Snps ◽

Resistance Trait

Powdery mildew (PM) is a common fungal disease infecting pepper plants worldwide. Molecular breeding of pepper cultivars with powdery mildew resistance is desirable for the economic improvement of pepper cultivation. In the present study, 188 F5 population derived from AR1 (PM resistant) and TF68 (PM sensitive) parents were subjected to high-throughput genotyping by sequencing (GBS) for the identification of single nucleotide polymorphism (SNP) markers. Further, the identified SNP markers were utilized for the construction of genetic linkage map and QTL analysis. Overall read mapping percentage of 87.29% was achieved in this study with the total length of mapped region ranging from 2,956,730 to 25,537,525 bp. A total of 41,111 polymorphic SNPs were identified, and a final of 1,841 SNPs were filtered for the construction of a linkage map. A total of 12 linkage groups were constructed corresponding to each chromosome with 1,308 SNP markers with the map length of 2506.8 cM. Further, two QTLs such as Pm-2.1 and Pm-5.1 were identified in chromosomes 2 and 5, respectively, for the PM resistance. Overall, the outcomes of the present endeavor can be utilized for the marker-assisted selection of pepper with powdery mildew-resistant trait.

Download Full-text

Detection of Quantitative Trait Loci (QTL) associated with the spring regrowth vigor trait in alfalfa (Medicago sativa L.)

10.21203/rs.3.rs-16909/v1 ◽

2020 ◽

Author(s):

Xueqian Jiang ◽

Fan Zhang ◽

Zhen Wang ◽

Ruicai Long ◽

Mingna Li ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Medicago Sativa ◽

Quantitative Trait ◽

Female Parent ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Phenotypic Data ◽

Single Nucleotide ◽

Trait Loci ◽

Medicago Sativa L

Abstract Background: Alfalfa ( Medicago sativa L.) is a perennial forage legume with a reputation as being the “queen of forage”. Spring regrowth vigor refers to the process of perennial alfalfa returning to growth after winter survival. The objective of this research was to identify candidate genes significantly associated with spring regrowth vigor.Results: We used a tetraploid alfalfa F1 population comprised of 392 progenies to identify quantitative trait loci (QTL) that control this trait. The F1 population phenotypic data were collected using a total of three environmental phenotypic data. The mapping population was genotyped using Genotyping-by-sequencing (GBS), and linkage maps were developed based on single nucleotide polymorphism (SNP) markers. Fifteen significant QTL for spring regrowth vigor were detected in both parents. Five QTL were identified in the male genetic map, while ten QTL were identified in the female. Four QTL were located on homolog 7D of the male parent, and two QTL were colocalized. Five QTL were mapped on homolog 6D of the female parent, and two QTL were colocalized.Conclusions: The QTL presented in this study can be used to improve the efficiency of alfalfa breeding programs and provide valuable resources for the genetic improvement of alfalfa using marker-assisted selection (MAS).β These authors contributed equally to this research. *Correspondence:Junmei [email protected]

Download Full-text