The Soybean High Density ‘Forrest’ by ‘Williams 82’ SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content

Isoflavones are secondary metabolites that are abundant in soybean and other legume seeds providing health and nutrition benefits for both humans and animals. The objectives of this study were to construct a single nucleotide polymorphism (SNP)-based genetic linkage map using the ‘Forrest’ by ‘Williams 82’ (F×W82) recombinant inbred line (RIL) population (n = 306); map quantitative trait loci (QTL) for seed daidzein, genistein, glycitein, and total isoflavone contents in two environments over two years (NC-2018 and IL-2020); identify candidate genes for seed isoflavone. The FXW82 SNP-based map was composed of 2075 SNPs and covered 4029.9 cM. A total of 27 QTL that control various seed isoflavone traits have been identified and mapped on chromosomes (Chrs.) 2, 4, 5, 6, 10, 12, 15, 19, and 20 in both NC-2018 (13 QTL) and IL-2020 (14 QTL). The six QTL regions on Chrs. 2, 4, 5, 12, 15, and 19 are novel regions while the other 21 QTL have been identified by other studies using different biparental mapping populations or genome-wide association studies (GWAS). A total of 130 candidate genes involved in isoflavone biosynthetic pathways have been identified on all 20 Chrs. and among them 16 have been identified and located within or close to the QTL identified in this study. Moreover, transcripts from four genes (Glyma.10G058200, Glyma.06G143000, Glyma.06G137100, and Glyma.06G137300) were highly abundant in Forrest and Williams 82 seeds. The identified QTL and four candidate genes will be useful in breeding programs to develop soybean cultivars with high beneficial isoflavone contents.

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Construction of a genetic linkage map, QTLs mapping for low salinity and growth-related traits and identification of the candidate genes in Pacific white shrimp (Litopenaeus vannamei)

Aquaculture Reports ◽

10.1016/j.aqrep.2021.100978 ◽

2022 ◽

Vol 22 ◽

pp. 100978

Author(s):

Bing Chen ◽

Ping Zhong ◽

Xiaopeng Wu ◽

Kai Peng ◽

Yuping Sun ◽

...

Keyword(s):

Linkage Map ◽

Candidate Genes ◽

Litopenaeus Vannamei ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Pacific White Shrimp ◽

White Shrimp ◽

Low Salinity ◽

Qtls Mapping

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

BMC Genomics ◽

10.1186/s12864-020-07115-7 ◽

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.

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A SNP genetic linkage map based on the ‘Hamilton’ by ‘Spencer’ recombinant inbred line population identified QTL for seed isoflavone contents in soybean

Plant Breeding ◽

10.1111/pbr.12298 ◽

2015 ◽

Vol 134 (5) ◽

pp. 580-588 ◽

Cited By ~ 7

Author(s):

Masum Akond ◽

Shiming Liu ◽

Stella K. Kantartzi ◽

Khalid Meksem ◽

Nacer Bellaloui ◽

...

Keyword(s):

Linkage Map ◽

Inbred Line ◽

Recombinant Inbred Line ◽

Recombinant Inbred Line Population ◽

Recombinant Inbred ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Seed Isoflavone

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

Thrombosis and Haemostasis ◽

10.1055/s-0038-1656070 ◽

1997 ◽

Vol 77 (05) ◽

pp. 0873-0878 ◽

Cited By ~ 9

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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Construction of the first high-density genetic linkage map and identification of seed yield-related QTLs and candidate genes in Elymus sibiricus, an important forage grass in Qinghai-Tibet Plateau

BMC Genomics ◽

10.1186/s12864-019-6254-4 ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Zongyu Zhang ◽

Wengang Xie ◽

Junchao Zhang ◽

Na Wang ◽

Yongqiang Zhao ◽

...

Keyword(s):

Linkage Map ◽

Candidate Genes ◽

Seed Yield ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

High Density ◽

Tibet Plateau ◽

Linkage Groups ◽

Seed Shattering ◽

Elymus Sibiricus

Abstract Background Elymus sibiricus is an ecologically and economically important perennial, self-pollinated, and allotetraploid (StStHH) grass, widely used for forage production and animal husbandry in Western and Northern China. However, it has low seed yield mainly caused by seed shattering, which makes seed production difficult for this species. The goals of this study were to construct the high-density genetic linkage map, and to identify QTLs and candidate genes for seed-yield related traits. Results An F2 mapping population of 200 individuals was developed from a cross between single genotype from “Y1005” and “ZhN06”. Specific-locus amplified fragment sequencing (SLAF-seq) was applied to construct the first genetic linkage map. The final genetic map included 1971 markers on the 14 linkage groups (LGs) and was 1866.35 cM in total. The length of each linkage group varied from 87.67 cM (LG7) to 183.45 cM (LG1), with an average distance of 1.66 cM between adjacent markers. The marker sequences of E. sibiricus were compared to two grass genomes and showed 1556 (79%) markers mapped to wheat, 1380 (70%) to barley. Phenotypic data of eight seed-related traits (2016–2018) were used for QTL identification. A total of 29 QTLs were detected for eight seed-related traits on 14 linkage groups, of which 16 QTLs could be consistently detected for two or three years. A total of 6 QTLs were associated with seed shattering. Based on annotation with wheat and barley genome and transcriptome data of abscission zone in E. sibiricus, we identified 30 candidate genes for seed shattering, of which 15, 7, 6 and 2 genes were involved in plant hormone signal transcription, transcription factor, hydrolase activity and lignin biosynthetic pathway, respectively. Conclusion This study constructed the first high-density genetic linkage map and identified QTLs and candidate genes for seed-related traits in E. sibiricus. Results of this study will not only serve as genome-wide resources for gene/QTL fine mapping, but also provide a genetic framework for anchoring sequence scaffolds on chromosomes in future genome sequence assembly of E. sibiricus.

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A high-density SNP-based genetic map in Pelteobagrus vachelli and mapping of growth, sex determination and hypoxia tolerance related loci

10.21203/rs.2.11007/v1 ◽

2019 ◽

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: As is known to all, when we are doing QTL fine mapping, analyzing comparative genome, identifying candidate genes, making marker-assisted selection in aquaculture species, the high-density genetic linkage map is of great significance. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters made it difficult to do traditional selective breeding based on phenotypes. For instance, potential problems include lacking in genomic resource which is in large scale and short of markers that is related tightly to 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. It is reflected that bu using comparative genome mapping, a large majority (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 gene 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.

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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

Frontiers in Marine Science ◽

10.3389/fmars.2021.713783 ◽

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.

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