Detection of QTLs in a Mediterranean climate associated with fire blight necrosis length in Pyrus communis using a high‐resolution genetic linkage map

Abstract High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly.

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Fine Mapping of the Leaf Rust Resistance Gene Lr65 in Spelt Wheat ‘Altgold’

Frontiers in Plant Science ◽

10.3389/fpls.2021.666921 ◽

2021 ◽

Vol 12 ◽

Author(s):

Qiang Zhang ◽

Wenxin Wei ◽

Xiangxi Zuansun ◽

Shengnan Zhang ◽

Chen Wang ◽

...

Keyword(s):

High Resolution ◽

Linkage Map ◽

Leaf Rust ◽

Resistance Gene ◽

Genetic Linkage ◽

Rust Resistance ◽

Genetic Linkage Map ◽

Reference Genome ◽

Leaf Rust Resistance ◽

Leaf Rust Resistance Gene

Wheat leaf rust (also known as brown rust), caused by the fungal pathogen Puccinia triticina Erikss. (Pt), is one by far the most troublesome wheat disease worldwide. The exploitation of resistance genes has long been considered as the most effective and sustainable method to control leaf rust in wheat production. Previously the leaf rust resistance gene Lr65 has been mapped to the distal end of chromosome arm 2AS linked to molecular marker Xbarc212. In this study, Lr65 was delimited to a 0.8 cM interval between flanking markers Alt-64 and AltID-11, by employing two larger segregating populations obtained from crosses of the resistant parent Altgold Rotkorn (ARK) with the susceptible parents Xuezao and Chinese Spring (CS), respectively. 24 individuals from 622 F2 plants of crosses between ARK and CS were obtained that showed the recombination between Lr65 gene and the flanking markers Alt-64 and AltID-11. With the aid of the CS reference genome sequence (IWGSC RefSeq v1.0), one SSR marker was developed between the interval matched to the Lr65-flanking marker and a high-resolution genetic linkage map was constructed. The Lr65 was finally located to a region corresponding to 60.11 Kb of the CS reference genome. The high-resolution genetic linkage map founded a solid foundation for the map-based cloning of Lr65 and the co-segregating marker will facilitate the marker-assisted selection (MAS) of the target gene.

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Construction of a high-density genetic linkage map in pear (Pyrus communis×Pyrus pyrifolia nakai) using SSRs and SNPs developed by SLAF-seq

Scientia Horticulturae ◽

10.1016/j.scienta.2017.02.015 ◽

2017 ◽

Vol 218 ◽

pp. 198-204 ◽

Cited By ~ 12

Author(s):

Long Wang ◽

Xiugen Li ◽

Lei Wang ◽

Huabai Xue ◽

Jun Wu ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Pyrus Communis ◽

High Density ◽

Pyrus Pyrifolia ◽

Pyrus Pyrifolia Nakai

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A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Cyprinus carpio)

Frontiers in Genetics ◽

10.3389/fgene.2021.778487 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiaofeng Zhang ◽

Peixian Luan ◽

Dingchen Cao ◽

Guo Hu

Keyword(s):

High Resolution ◽

Linkage Map ◽

Common Carp ◽

Fine Mapping ◽

Cyprinus Carpio ◽

Feed Efficiency ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

High Density ◽

Feed Conversion

Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9–15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.

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