scholarly journals Construction of a Genetic Linkage Map Based on SNP Markers, QTL Mapping and Detection of Candidate Genes of Growth-Related Traits in Pacific Abalone Using Genotyping-by-Sequencing

2021 ◽  
Vol 8 ◽  
Author(s):  
Kang Hee Kho ◽  
Zahid Parvez Sukhan ◽  
Shaharior Hossen ◽  
Yusin Cho ◽  
Soo Cheol Kim ◽  
...  
Keyword(s):  
Linkage Map ◽  
Candidate Genes ◽  
Genetic Linkage ◽  
Growth Regulation ◽  
Molecular Breeding ◽  
Genetic Linkage Map ◽  
Genotyping By Sequencing ◽  
Breeding Program ◽  
Potential Candidate ◽  
Pacific Abalone

Pacific abalone (Haliotis discus hannai) is a commercially important high valued molluscan species. Its wild population has decreased in recent years. It is widely cultured in Korea. Traditional breeding programs have been implemented for hatchery production of abalone seeds. To obtain more genetic information for its molecular breeding program, a high-density linkage map and quantitative trait locus (QTL) for three growth-related traits was constructed for Pacific abalone. F1 cross population with two parents were sampled to construct the linkage map using genotyping by sequencing (GBS). A total of 664,630,534 clean reads and 56,686 SNPs were generated and 3,345 segregating SNPs were used to construct a consensus linkage map. The map spanned 1,747.023 cM with 18 linkage groups and an average interval of 0.55 cM. QTL analysis revealed two significant QTL in LG10 on the consensus linkage map of each growth-related trait. Both QTLs were located in the telomere region of the chromosome. Moreover, four potential candidate genes for growth-related traits were identified in the QTL region. Expression analysis revealed that these identified genes are involved in growth regulation of abalone. The newly constructed genetic linkage map, growth-related QTLs and potential candidate genes identified in the present study can be used as valuable genetic resources for marker-assisted selection (MAS) of Pacific abalone in molecular breeding program.

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

scholarly journals A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guosong Zhang ◽  
Jie Li ◽  
Jiajia Zhang ◽  
Xia Liang ◽  
Tao Wang ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Candidate Genes ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Hypoxia Tolerance ◽  
Genome Wide ◽  
Pelteobagrus Vachelli

Abstract Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. Results By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

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 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.

scholarly journals Construction of a high-density genetic linkage map and mapping of quantitative trait loci for growth-related traits in silver carp (Hypophthalmichthys molitrix)

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Xinhua Wang ◽  
Haiyang Liu ◽  
Meixia Pang ◽  
Beide Fu ◽  
Xiaomu Yu ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Linkage Map ◽  
Quantitative Trait ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Growth Traits ◽  
Silver Carp ◽  
High Density ◽  
Potential Candidate ◽  
Hypophthalmichthys Molitrix

AbstractHigh-density genetic map and quantitative trait loci (QTL) mapping are powerful tools for identifying genomic regions that may be responsible for such polygenic trait as growth. A high-density genetic linkage map was constructed by sequencing 198 individuals in a F1 family of silver carp (Hypophthalmichthys molitrix) in this study. This genetic map spans a length of 2,721.07 cM with 3,134 SNPs distributed on 24 linkage groups (LGs). Comparative genomic mapping presented a high level of syntenic relationship between silver carp and zebrafish. We detected one major and nineteen suggestive QTL for 4 growth-related traits (body length, body height, head length and body weight) at 6, 12 and 18 months post hatch (mph), explaining 10.2~19.5% of phenotypic variation. All six QTL for growth traits of 12 mph generally overlapped with QTL for 6 mph, while the majority of QTL for 18 mph were identified on two additional LGs, which may reveal a different genetic modulation during early and late muscle growth stages. Four potential candidate genes were identified from the QTL regions by homology searching of marker sequences against zebrafish genome. Hepcidin, a potential candidate gene identified from a QTL interval on LG16, was significantly associated with growth traits in the analyses of both phenotype-SNP association and mRNA expression between small-size and large-size groups of silver carp. These results provide a basis for elucidating the genetic mechanisms for growth and body formation in silver carp, a world aquaculture fish.

Location on the Human Genetic Linkage Map of 26 Genes Involved in Blood Coagulation

1997 ◽  
Vol 77 (05) ◽  
pp. 0873-0878 ◽  
Author(s):  
Bobby P C Koeleman ◽  
Pieter H Reitsma ◽  
Egbert Bakker ◽  
Rogier M Bertina
Keyword(s):  
Linkage Map ◽  
Blood Coagulation ◽  
Candidate Genes ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Coagulation Cascade ◽  
Candidate Gene Approach ◽  
Genotype Data ◽  
Genetic Linkage Analysis ◽  
Linkage Maps

SummarySeveral human genetic linkage maps have been constructed as part of the Human Genome Project. These maps show the positional order of closely linked, highly informative AC-repeat polymorphisms on each human chromosome, and are extremely useful in genetic linkage analysis of inheritable diseases. For a candidate gene approach the current linkage maps are less useful, since they consist mainly of anonymous markers rather than of specific genes. This situation also applies for inheritable disorders of blood coagulation. Numerous genes are involved in the blood coagulation cascade and its regulation, and can be considered as candidate genes for unexplained haemophilia and thrombophilia. We have selected 29 candidate genes that seem to be the ones most likely to be involved in thrombophilia. For 19 genes genotype data were already present in the CEPH database (version 7.0). We typed 7 additional genes in the CEPH reference families, i.e. the factor V, factor XII, protein C, protein S, prothrombin, thrombomodulin, and heparin cofactor II gene. The genotype data were used to integrate these 26 genes in the current genetic linkage map, and to identify closely linked AC-repeat polymorphisms. This information will benefit the investigation of inheritable disorders of blood coagulation, especially thrombophilia.

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