scholarly journals Construction of an Onion (Allium cepa L.) Genetic Linkage Map Using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content

Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 616 ◽  
Author(s):  
Yousoo Choi ◽  
Sunggil Kim ◽  
Jundae Lee
Keyword(s):  
Linkage Map ◽  
Reference Gene ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Genotyping By Sequencing ◽  
Anthocyanin Synthesis ◽  
Anthocyanin Content ◽  
Marker Development ◽  
Linkage Groups ◽  
Gene Set

Anthocyanins, the pigmented flavonoids responsible for red and blue colors in horticultural products, promote human health by preventing cancers and lowering the risk of cardiovascular disease. Red onions contain several cyanidin- and peonidin-based anthocyanins. In this study, we constructed a single-nucleotide polymorphism (SNP)-based genetic linkage map in an F2 segregating population derived from a cross between the inbred line ‘SP3B’ (yellow bulb) and the doubled haploid line ‘H6′ (red bulb) to identify quantitative trait loci (QTLs) for total anthocyanin content of onion bulbs using a genotyping-by-sequencing (GBS) analysis based on a reference gene set. A total of 101.9 Gbp of raw sequences were generated using an Illumina HiSeq 2500 system and a total of 1625 SNP loci were identified with the criteria of three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 319 GBS-based SNP loci and 34 high-resolution melting (HRM) markers was constructed with eight linkage groups and a total genetic distance of 881.4 cM. In addition, the linkage groups were assigned to corresponding chromosomes by comparison with the reference genetic map OH1×5225 through marker development based on common transcripts. The analysis revealed one major QTL, qAS7.1, for anthocyanin synthesis and two significant QTLs, qAC4.1 and qAC4.2, for anthocyanin content. The QTL qAS7.1, located on chromosome 7 with a phenotypic variation of 87.61%, may be a dihydroflavonol 4-reductase (DFR) gene that determines whether the bulb color is red or yellow. The QTLs qAC4.1 and qAC4.2 are separately positioned on chromosome 4 with R2 values of 19.43% and 26.28%, respectively. This map and QTL information will contribute to marker development and breeding for high anthocyanin content in bulb onion.

Construction of genetic linkage map using genotyping-by-sequencing and identification of QTLs associated with leaf color in spinach

Euphytica ◽  
2018 ◽  
Vol 214 (12) ◽  
Author(s):  
Xiaofeng Cai ◽  
Chenxi Xu ◽  
Xiaoli Wang ◽  
Shui Wang ◽  
Zhonghua Zhang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Genotyping By Sequencing ◽  
Leaf Color

Genotyping-by-sequencing for construction of a new genetic linkage map and QTL analysis of growth-related traits in Pacific bluefin tuna

2017 ◽  
Vol 49 (3) ◽  
pp. 1293-1301 ◽  
Author(s):  
Tsubasa Uchino ◽  
Erina Hosoda ◽  
Yoji Nakamura ◽  
Motoshige Yasuike ◽  
Miyuki Mekuchi ◽  
...  
Keyword(s):  
Linkage Map ◽  
Qtl Analysis ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Genotyping By Sequencing ◽  
Bluefin Tuna ◽  
Pacific Bluefin Tuna

scholarly journals Genetic Linkage Map of the Edible BasidiomycetePleurotus ostreatus

2000 ◽  
Vol 66 (12) ◽  
pp. 5290-5300 ◽  
Author(s):  
Luis M. Larraya ◽  
G�mer P�rez ◽  
Enrique Ritter ◽  
Antonio G. Pisabarro ◽  
Lucı́a Ramı́rez
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Gene Sequence ◽  
Genetic Linkage Map ◽  
Fragment Length Polymorphism ◽  
Individual Cell ◽  
Random Amplified Polymorphic Dna ◽  
Rrna Gene ◽  
Linkage Groups ◽  
Rrna Gene Sequence

ABSTRACT We have constructed a genetic linkage map of the edible basidiomycete Pleurotus ostreatus (var. Florida). The map is based on the segregation of 178 random amplified polymorphic DNA and 23 restriction fragment length polymorphism markers; four hydrophobin, two laccase, and two manganese peroxidase genes; both mating type loci; one isozyme locus (est1); the rRNA gene sequence; and a repetitive DNA sequence in a population of 80 sibling monokaryons. The map identifies 11 linkage groups corresponding to the chromosomes ofP. ostreatus, and it has a total length of 1,000.7 centimorgans (cM) with an average of 35.1 kbp/cM. The map shows a high correlation (0.76) between physical and genetic chromosome sizes. The number of crossovers observed per chromosome per individual cell is 0.89. This map covers nearly the whole genome of P. ostreatus.

A genetic linkage map for Stevia rebaudiana

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 657-661 ◽  
Author(s):  
Y Yao ◽  
M Ban ◽  
J Brandle
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Average Distance ◽  
Stevia Rebaudiana ◽  
Linkage Groups ◽  
Genome Map ◽  
High Level ◽  
Map Distance

To lay a foundation for molecular breeding efforts, the first genetic linkage map for Stevia rebaudiana has been constructed using segregation data from a pseudo test-cross F1 population. A total of 183 randomly amplified polymorphic DNA (RAPD) markers were analysed and assembled into 21 linkage groups covering a total distance of 1389 cM, with an average distance between markers of of 7.6 cM. The 11 largest linkage groups consisted of 4-19 loci, ranged in length from 56 to 174 cM, and accounted for 75% of the total map distance. Fifteen RAPD loci were found to be unlinked. From the 521 primers showing amplification products, 185 (35.5%) produced a total of 293 polymorphic fragments, indicating a high level of genetic diversity in stevia. Most of the RAPD markers in stevia segregated in normal Mendelian fashion.Key words: stevia, open-pollinated, genome map, RAPD.

Mapping of quantitative trait loci underlying resistance to cassava anthracnose disease

2015 ◽  
Vol 154 (7) ◽  
pp. 1209-1217 ◽  
Author(s):  
A. BOONCHANAWIWAT ◽  
S. SRAPHET ◽  
S. WHANKAEW ◽  
O. BOONSENG ◽  
D. R. SMITH ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Linkage Map ◽  
Dna Markers ◽  
Quantitative Trait ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Gene Annotation ◽  
Linkage Groups ◽  
Anthracnose Disease ◽  
Trait Loci

SUMMARYCassava (Manihot esculenta Crantz) is an economically important root crop in Thailand, which is ranked the world's top cassava exporting country. Production of cassava can be hampered by several pathogens and pests. Cassava anthracnose disease (CAD) is an important disease caused by the fungus Colletotrichum gloeosporioides f. sp. manihotis. The pathogen causes severe stem damage resulting in yield reductions and lack of stem cuttings available for planting. Molecular studies of cassava response to CAD will provide useful information for cassava breeders to develop new varieties with resistance to the disease. The current study aimed to identify quantitative trait loci (QTL) and DNA markers associated with resistance to CAD. A total of 200 lines of two F1 mapping populations were generated by reciprocal crosses between the varieties Huabong60 and Hanatee. The F1 samples were genotyped based on simple sequence repeat (SSR) and expressed sequence tag-SSR markers and a genetic linkage map was constructed using the JoinMap®/version3·0 program. The results showed that the map consisted of 512 marker loci distributed on 24 linkage groups with a map length of 1771·9 centimorgan (cM) and a mean interval between markers of 5·7 cM. The genetic linkage map was integrated with phenotypic data for the response to CAD infection generated by a detached leaf assay test. A total of three QTL underlying the trait were identified on three linkage groups using the MapQTL®/version4·0 program. Those DNA markers linked to the QTL that showed high statistically significant values with the CAD resistance trait were identified for gene annotation analysis and 23 candidate resistance genes to CAD infection were identified.

scholarly journals Development of a genetic linkage map for Sharon goatgrass (Aegilops sharonensis) and mapping of a leaf rust resistance gene

Genome ◽  
2013 ◽  
Vol 56 (7) ◽  
pp. 367-376 ◽  
Author(s):  
P.D. Olivera ◽  
A. Kilian ◽  
P. Wenzl ◽  
B.J. Steffenson
Keyword(s):  
Linkage Map ◽  
Leaf Rust ◽  
Resistance Genes ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Chromosomal Location ◽  
Dominant Gene ◽  
Leaf Rust Resistance Gene ◽  
Linkage Groups ◽  
Aegilops Sharonensis

Aegilops sharonensis (Sharon goatgrass), a diploid wheat relative, is known to be a rich source of disease resistance genes for wheat improvement. To facilitate the transfer of these genes into wheat, information on their chromosomal location is important. A genetic linkage map of Ae. sharonensis was constructed based on 179 F2 plants derived from a cross between accessions resistant (1644) and susceptible (1193) to wheat leaf rust. The linkage map was based on 389 markers (377 Diversity Arrays Technology (DArT) and 12 simple sequence repeat (SSR) loci) and was comprised of 10 linkage groups, ranging from 2.3 to 124.6 cM. The total genetic length of the map was 818.0 cM, with an average interval distance between markers of 3.63 cM. Based on the chromosomal location of 115 markers previously mapped in wheat, the four linkage groups of A, B, C, and E were assigned to Ae. sharonensis (Ssh) and homoeologous wheat chromosomes 6, 1, 3, and 2. The single dominant gene (designated LrAeSh1644) conferring resistance to leaf rust race THBJ in accession 1644 was positioned on linkage group A (chromosome 6Ssh) and was flanked by DArT markers wpt-9881 (at 1.9 cM distal from the gene) and wpt-6925 (4.5 cM proximal). This study clearly demonstrates the utility of DArT for genotyping uncharacterized species and tagging resistance genes where pertinent genomic information is lacking.

A genetic linkage map of tetraploid orchardgrass (Dactylis glomerata L.) and quantitative trait loci for heading date

Genome ◽  
2012 ◽  
Vol 55 (5) ◽  
pp. 360-369 ◽  
Author(s):  
Wengang Xie ◽  
Joseph G. Robins ◽  
B. Shaun Bushman
Keyword(s):  
Quantitative Trait Loci ◽  
Linkage Map ◽  
Quantitative Trait ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Heading Date ◽  
Dactylis Glomerata ◽  
Linkage Groups ◽  
Trait Loci ◽  
Dactylis Glomerata L

Orchardgrass ( Dactylis glomerata L.), or cocksfoot, is indigenous to Eurasia and northern Africa, but has been naturalized on nearly every continent and is one of the top perennial forage grasses grown worldwide. To improve the understanding of genetic architecture of orchardgrass and provide a template for heading date candidate gene search in this species, the goals of the present study were to construct a tetraploid orchardgrass genetic linkage map and identify quantitative trait loci associated with heading date. A combination of SSR markers derived from an orchardgrass EST library and AFLP markers were used to genotype an F1 population of 284 individuals derived from a very late heading Dactylis glomerata subsp. himalayensis parent and an early to mid-heading Dactylis glomerata subsp. aschersoniana parent. Two parental maps were constructed with 28 cosegregation groups and seven consensus linkage groups each, and homologous linkage groups were tied together by 38 bridging markers. Linkage group lengths varied from 98 to 187 cM, with an average distance between markers of 5.5 cM. All but two mapped SSR markers had homologies to physically mapped rice (Oryza sativa L.) genes, and six of the seven orchardgrass linkage groups were assigned based on this putative synteny with rice. Quantitative trait loci were detected for heading date on linkage groups 2, 5, and 6 in both parental maps, explaining between 12% and 24% of the variation.

scholarly journals Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12390
Author(s):  
Yaqun Zhang ◽  
Chuantao Zhang ◽  
Na Yao ◽  
Jingxian Huang ◽  
Xiangshan Sun ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Molecular Mechanisms ◽  
Genetic Linkage Map ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Nucleotide Polymorphisms ◽  
Penaeus Japonicus ◽  
Genetic Mechanisms

Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.

Linkage of random amplified polymorphic DNA, isozyme and morphological markers in grasspea (Lathyrus sativus)

1999 ◽  
Vol 133 (4) ◽  
pp. 389-395 ◽  
Author(s):  
M. A. CHOWDHURY ◽  
A. E. SLINKARD
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Average Distance ◽  
Random Amplified Polymorphic Dna ◽  
Lathyrus Sativus ◽  
Morphological Markers ◽  
Linkage Studies ◽  
Linkage Groups

We constructed a genetic linkage map of grasspea (Lathyrus sativus L.; 2n = 14) from 100 F2 individuals derived from a cross between PI 426891.1.3 and PI 283564c.3.2. A total of 71 RAPD, three isozyme and one morphological markers segregated in the F2 progeny. A small fraction of markers (12%) deviated significantly from the expected Mendelian ratio (1[ratio ]2[ratio ]1 or 3[ratio ]1). Out of 75 markers, 69 (one morphological, three isozyme and 65 RAPD markers) were assigned to 14 linkage groups comprising 898 cM. The average distance between two adjacent markers was 17·2 cM. The present linkage map will serve as a reference point for further linkage studies in grasspea.

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