A genome-wide genetic linkage map and reference quality genome sequence for a new race in the wheat pathogen Pyrenophora tritici-repentis

2021 ◽  
pp. 103571
Author(s):  
Gayan K. Kariyawasam ◽  
Nathan Wyatt ◽  
Gongjun Shi ◽  
Sanzhen Liu ◽  
Changhui Yan ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genome Sequence ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Pyrenophora Tritici Repentis ◽  
Genome Wide ◽  
A Genome ◽  
Reference Quality ◽  
New Race

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.

scholarly journals Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of the Legume Crop Species Lupinus angustifolius L

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e64799 ◽  
Author(s):  
Huaan Yang ◽  
Ye Tao ◽  
Zequn Zheng ◽  
Qisen Zhang ◽  
Gaofeng Zhou ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genome Sequence ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Draft Genome ◽  
Lupinus Angustifolius ◽  
Draft Genome Sequence ◽  
Crop Species ◽  
Legume Crop

Integration of Brassica A genome genetic linkage map between Brassica napus and B. rapa

Genome ◽  
2008 ◽  
Vol 51 (3) ◽  
pp. 169-176 ◽  
Author(s):  
Keita Suwabe ◽  
Colin Morgan ◽  
Ian Bancroft
Keyword(s):  
Molecular Markers ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Linkage Groups ◽  
Indel Markers ◽  
A Genome ◽  
High Level ◽  
High Degree ◽  
Genetic Integration

An integrated linkage map between B. napus and B. rapa was constructed based on a total of 44 common markers comprising 41 SSR (33 BRMS, 6 Saskatoon, and 2 BBSRC) and 3 SNP/indel markers. Between 3 and 7 common markers were mapped onto each of the linkage groups A1 to A10. The position and order of most common markers revealed a high level of colinearity between species, although two small regions on A4, A5, and A10 revealed apparent local inversions between them. These results indicate that the A genome of Brassica has retained a high degree of colinearity between species, despite each species having evolved independently after the integration of the A and C genomes in the amphidiploid state. Our results provide a genetic integration of the Brassica A genome between B. napus and B. rapa. As the analysis employed sequence-based molecular markers, the information will accelerate the exploitation of the B. rapa genome sequence for the improvement of oilseed rape.

scholarly journals Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map

Mycobiology ◽  
2021 ◽  
pp. 1-15
Author(s):  
Wan-Zhu Jiang ◽  
Fang-Jie Yao ◽  
Ming Fang ◽  
Li-Xin Lu ◽  
You-Min Zhang ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genome Sequence ◽  
Genetic Linkage ◽  
Genetic Linkage Map

scholarly journals Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Jinsong Xu ◽  
Xiaoju Qian ◽  
Xiaofeng Wang ◽  
Ruiyuan Li ◽  
Xiaomao Cheng ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Linkage Map ◽  
Ssr Markers ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
A Genome

A genetic linkage map of an apple rootstock progeny anchored to the Malus genome sequence

2012 ◽  
Vol 8 (5) ◽  
pp. 991-1002 ◽  
Author(s):  
F. Fernández-Fernández ◽  
L. Antanaviciute ◽  
M. M. van Dyk ◽  
K. R. Tobutt ◽  
K. M. Evans ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genome Sequence ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Apple Rootstock

Construction of genetic linkage map and mapping of QTL for seed color in Brassica rapa

Genome ◽  
2012 ◽  
Vol 55 (12) ◽  
pp. 813-823 ◽  
Author(s):  
Berisso Kebede ◽  
Kuljit Cheema ◽  
David L. Greenshields ◽  
Changxi Li ◽  
Gopalan Selvaraj ◽  
...  
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Brassica Rapa ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Recombinant Inbred Lines ◽  
Phenotypic Variance ◽  
Environment Interaction ◽  
Seed Color ◽  
A Genome

A genetic linkage map of Brassica rapa L. was constructed using recombinant inbred lines (RILs) derived from a cross between yellow-seeded cultivar Sampad and a yellowish brown seeded inbred line 3-0026.027. The RILs were evaluated for seed color under three conditions: field plot, greenhouse, and controlled growth chambers. Variation for seed color in the RILs ranged from yellow, like yellow sarson, to dark brown/black even though neither parent had shown brown/black colored seeds. One major QTL (SCA9-2) and one minor QTL (SCA9-1) on linkage group (LG) A9 and two minor QTL (SCA3-1, SCA5-1) on LG A3 and LG A5, respectively, were detected. These collectively explained about 67% of the total phenotypic variance. SCA9-2 mapped in the middle of LG A9, explained about 55% phenotypic variance, and consistently expressed in all environments. The second QTL on LG A9 was ∼70 cM away from SCA9-2, suggesting that independent assortment of these QTLs is possible. A digenic epistatic interaction was found between the two main effect QTL on LG A9; and the epistasis × environment interaction was nonsignificant, suggesting stability of the interaction across the environments. The QTL effect on LG A9 was validated using simple sequence repeat (SSR) markers from the two QTL regions of this LG on a B1S1 population (F1 backcrossed to Sampad followed by self-pollination) segregating for brown and yellow seed color, and on their self-pollinated progenies (B1S2). The SSR markers from the QTL region SCA9-2 showed a stronger linkage association with seed color as compared with the marker from SCA9-1. This suggests that the QTL SCA9-2 is the major determinant of seed color in the A genome of B. rapa.

Genome-wide identification of silique-related traits based on high-density genetic linkage map in Brassica napus

2019 ◽  
Vol 39 (6) ◽  
Author(s):  
Weiguo Zhao ◽  
Lina Zhang ◽  
Hongbo Chao ◽  
Hao Wang ◽  
Na Ta ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Linkage Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Genome Wide

scholarly journals A Second-Generation Genetic Linkage Map of the Domestic Dog, Canis familiaris

Genetics ◽  
1999 ◽  
Vol 151 (2) ◽  
pp. 803-820 ◽  
Author(s):  
Mark W Neff ◽  
Karl W Broman ◽  
Cathryn S Mellersh ◽  
Kunal Ray ◽  
Gregory M Acland ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Positional Cloning ◽  
Genetic Linkage Map ◽  
Domestic Dog ◽  
Disease Genes ◽  
A Genome ◽  
High Incidence ◽  
Genetic Length ◽  
And Behavior

Abstract Purebred strains, pronounced phenotypic variation, and a high incidence of heritable disease make the domestic dog uniquely suited to complement genetic analyses in humans and mice. A comprehensive genetic linkage map would afford many opportunities in dogs, ranging from the positional cloning of disease genes to the dissection of quantitative differences in size, shape, and behavior. Here we report a canine linkage map with the number of mapped loci expanded to 276 and 10-cM coverage extended to 75–90% of the genome. Most of the 38 canine autosomes are likely represented in the collection of 39 autosomal linkage groups. Eight markers were sufficiently informative to detect linkage at distances of 10–13 cM, yet remained unlinked to any other marker. Taken together, the results suggested a genome size of about 27 M. As in other species, the genetic length varied between sexes, with the female autosomal distance being ∼1.4-fold greater than that of male meioses. Fifteen markers anchored well-described genes on the map, thereby serving as landmarks for comparative mapping in dogs. We discuss the utility of the current map and outline steps necessary for future map improvement.

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