scholarly journals Melon Genome Regions Associated with TGR-1551-Derived Resistance to Cucurbit yellow stunting disorder virus

2020 ◽  
Vol 21 (17) ◽  
pp. 5970
Author(s):  
Ana Pérez-de-Castro ◽  
María López-Martín ◽  
Cristina Esteras ◽  
Ana Garcés-Claver ◽  
Francisco Javier Palomares-Ríus ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Genotyping By Sequencing ◽  
Major Effect ◽  
Snp Markers ◽  
Limiting Factors ◽  
Susceptible Cultivar ◽  
Chromosome 5 ◽  
Melon Genome ◽  
Or Genes ◽  
Candidate Interval

Cucurbit yellow stunting disorder virus (CYSDV) is one of the main limiting factors of melon cultivation worldwide. To date, no commercial melon cultivars resistant to CYSDV are available. The African accession TGR-1551 is resistant to CYSDV. Two major quantitative trait loci (QTLs) have been previously reported, both located near each other in chromosome 5. With the objective of further mapping the gene or genes responsible of the resistance, a recombinant inbred line (RIL) population derived from the cross between TGR-1551 and the susceptible cultivar ‘Bola de Oro’ was evaluated for resistance to CYSDV in five different assays and genotyped in a genotyping by sequencing (GBS) analysis. The major effect of one of the two QTLs located on chromosome 5 was confirmed in the multienvironment RIL assay and additionally verified through the analysis of three segregating BC1S1 populations derived from three resistant RILs. Furthermore, progeny test using the offspring of selected BC3 plants allowed the narrowing of the candidate interval to a 700 kb region. The SNP markers identified in this work will be useful in marker-assisted selection in the context of introgression of CYSDV resistance in elite cultivars.

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 Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengjie Chen ◽  
Dengguo Tang ◽  
Jixing Ni ◽  
Peng Li ◽  
Le Wang ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Inbred Lines ◽  
Average Density ◽  
Snp Markers ◽  
Data Sets ◽  
Rna Seq ◽  
Specific Pcr ◽  
Maize Inbred Lines ◽  
Allele Specific ◽  
Allele Specific Pcr

Abstract Background Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines. Results A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic. Conclusions These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.

scholarly journals Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1042
Author(s):  
Zhuoying Weng ◽  
Yang Yang ◽  
Xi Wang ◽  
Lina Wu ◽  
Sijie Hua ◽  
...  
Keyword(s):  
Fishery Management ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Individual Identification ◽  
Pedigree Information ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Polymorphic Snps ◽  
Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

scholarly journals 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®

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.

scholarly journals Insights into the Genetic Architecture of Phenotypic Stability Traits in Winter Wheat

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 368 ◽  
Author(s):  
Dennis Lozada ◽  
Arron Carter
Keyword(s):  
Winter Wheat ◽  
Pacific Northwest ◽  
Genetic Architecture ◽  
Heading Date ◽  
Major Effect ◽  
Snp Markers ◽  
Genetic Loci ◽  
Phenotypic Stability ◽  
Trait Stability ◽  
Genetic Complexity

Examining the architecture of traits through genomics is necessary to gain a better understanding of the genetic loci affecting important traits to facilitate improvement. Genomewide association study (GWAS) and genomic selection (GS) were implemented for grain yield, heading date, and plant height to gain insights into the genetic complexity of phenotypic stability of traits in a diverse population of US Pacific Northwest winter wheat. Analysis of variance using the Additive Main Effect and Multiplicative Interaction (AMMI) approach revealed significant genotype and genotype by environment interactions. GWAS identified 12 SNP markers distributed across 10 chromosomes affecting variation for both trait and phenotypic stability, indicating potential pleiotropic effects and signifying that similar genetic loci could be associated with different aspects of stability. The lack of stable and major effect loci affecting phenotypic variation supports the complexity of stability of traits. Accuracy of GS was low to moderate, between 0.14 and 0.66, indicating that phenotypic stability is under genetic control. The moderate to high correlation between trait and trait stability suggests the potential of simultaneous selection for trait and trait stability. Our results demonstrate the complex genetic architecture of trait stability and show the potential for improving stability in winter wheat using genomic-assisted approaches.

scholarly journals Genetic Analysis and Fine Mapping of a Spontaneously Mutated Male Sterility Gene in Brassica rapa ssp. chinensis

2020 ◽  
Vol 10 (4) ◽  
pp. 1309-1318
Author(s):  
Tzu-Kai Lin ◽  
Ya-Ping Lin ◽  
Shun-Fu Lin
Keyword(s):  
Male Sterility ◽  
Fine Mapping ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Hybrid Seed Production ◽  
Spontaneous Mutant ◽  
Male Sterile ◽  
Sterility Gene ◽  
Intron 4 ◽  
Male Sterility Gene

Male sterility has been widely used in hybrid seed production in Brassica, but not in B. rapa ssp. chinensis, and genetic models of male sterility for this subspecies are unclear. We discovered a spontaneous mutant in B. rapa ssp. chinensis. A series of progeny tests indicated that male sterility in B. rapa ssp. chinensis follows a three-allele model with BrMsa, BrMsb, and BrMsc. The male sterility locus has been mapped to chromosome A07 in BC1 and F2 populations through genotyping by sequencing. Fine mapping in a total of 1,590 F2 plants narrowed the male sterility gene BrMs to a 400 kb region, with two SNP markers only 0.3 cM from the gene. Comparative gene mapping shows that the Ms gene in B. rapa ssp. pekinensis is different from the BrMs gene of B. rapa ssp. chinensis, despite that both genes are located on chromosome A07. Interestingly, the DNA sequence orthologous to a male sterile gene in Brassica napus, BnRf, is within 400 kb of the BrMs locus. The BnRf orthologs of B. rapa ssp. chinensis were sequenced, and one KASP marker (BrMs_indel) was developed for genotyping based on a 14 bp indel at intron 4. Cosegregation of male sterility and BrMs_indel genotypes in the F2 population indicated that BnRf from B. napus and BrMs from B. rapa are likely to be orthologs. The BrMs_indel marker developed in this study will be useful in marker-assisted selection for the male sterility trait.

Two closely linked interactive blood pressure QTL on rat chromosome 5 defined using congenic Dahl rats

2002 ◽  
Vol 8 (2) ◽  
pp. 81-86 ◽  
Author(s):  
Michael R. Garrett ◽  
John P. Rapp
Keyword(s):  
Blood Pressure ◽  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Congenic Strain ◽  
Major Effect ◽  
Large Region ◽  
Chromosome 5 ◽  
Low Blood Pressure ◽  
Trait Locus

Previously we reported the construction of a congenic strain, S.LEW( 5 ), spanning a large region of rat chromosome 5. The Lewis (LEW) strain was the donor, and the Dahl salt-sensitive (S) strain was the recipient. The congenic strain included a blood pressure quantitative trait locus (QTL). In the present work, a series of nine congenic substrains were constructed from S.LEW( 5 ) which defined two closely linked blood pressure QTL in the region previously thought to contain only one. LEW low-blood-pressure alleles at both QTL were required for a major effect on blood pressure. Neither LEW allele alone had a significant effect on blood pressure. The two QTL were localized to regions 6.3 and 4.6 cM, and these were 1.0 cM apart.

Correlation Analysis between MyoG Gene Polymorphism and Carcass Characteristics of Egg quails

2020 ◽  
Author(s):  
Jun Yan Bai ◽  
Xiao Ping Jia ◽  
Jun Hao Lu ◽  
Shuai Yang ◽  
You Zhi Pang ◽  
...  
Keyword(s):  
Heart Rate ◽  
Gene Polymorphism ◽  
Control Region ◽  
Marker Assisted Selection ◽  
Sexual Maturity ◽  
Carcass Characteristics ◽  
Snp Markers ◽  
Muscle Weight ◽  
Leg Muscle ◽  
Production Period

Quail is extensively reared in China for characteristic of quick growth, small fodder consumption, early sexual maturity, high egg output and short production period. In this study, the SNP markers in 5’ regulation regions of cytogenin gene (MyoG) among China yellow quail, Beijing white quail and Korean quail were detected by PCR-SSCP method. Moreover, correlations of MyoG 5’ regulation regions with carcass characteristics of quail were analyzed. Results demonstrated thatin egg quail group, six genotypes were detected in Locus A in the control region of MyoG 5’, including AA, BB, CC, AB, AC and BC. The highest frequencies of CC in China yellow quail, Beijing white quail and Korean quail were 0.323, 0.366 and 0.444, respectively. A total of 9 genotypes were detected in locus B in egg quail group, which were AA, BB, CC, DD, EE, AB, AC, AD and AE. AA showed the highest frequency in China yellow quail, Beijing white quail and Korean quail, which were 0.493, 0.385 and 0.406, respectively. There was significant correlation between locus A and leg muscle rate of egg quail (plessthan0.05). Locus B presented significant correlations with carcass net weight, leg muscle weight, dressing percentage, whole net carcass rate and heart rate (plessthan0.05). Loci A and B in the control region of MyoG 5’ can be used as the molecular marker of carcass characteristics of egg quails during marker assisted selection.

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