Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

Nie, Hongtao; Yan, Xiwu; Huo, Zhongming; Jiang, Liwen; Chen, Peng; Liu, Hui; Ding, Jianfeng; Yang, Feng

doi:10.1038/s41598-017-00246-0

Cited by 30 publications

(23 citation statements)

References 54 publications

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“…Reduced-representation sequencing techniques such as GBS or RAD-seq will likely be important for future genomics-based selection in molluscs, as such techniques allow for pedigree reconstruction, estimation of trait heritability, genetic map construction, identification of QTL, and estimation of genomic breeding values in the same experiment (Palaiokostas et al, 2016 ; Robledo et al, 2017 ). QTL mapping studies involving GBS or RAD-seq have been published for scallops (Jiao et al, 2014 ), oysters (Li and He, 2014 ; Shi et al, 2014 ; Wang et al, 2016 ), clams (Nie et al, 2017 ), and abalone (Ren et al, 2016 ). Recently, the feasibility of GS using 2b-RAD (Wang et al, 2012 ) was demonstrated in an experiment involving Yesso scallops ( Patinopectin yessoensis ; Dou et al, 2016 ).…”

Section: Opportunities For Genomics-based Selectionmentioning

confidence: 99%

Genomic Tools and Selective Breeding in Molluscs

Hollenbeck

Johnston

2018

Front. Genet.

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The production of most farmed molluscs, including mussels, oysters, scallops, abalone, and clams, is heavily dependent on natural seed from the plankton. Closing the lifecycle of species in hatcheries can secure independence from wild stocks and enables long-term genetic improvement of broodstock through selective breeding. Genomic techniques have the potential to revolutionize hatchery-based selective breeding by improving our understanding of the characteristics of mollusc genetics that can pose a challenge for intensive aquaculture and by providing a new suite of tools for genetic improvement. Here we review characteristics of the life history and genetics of molluscs including high fecundity, self-fertilization, high genetic diversity, genetic load, high incidence of deleterious mutations and segregation distortion, and critically assess their impact on the design and effectiveness of selective breeding strategies. A survey of the results of current breeding programs in the literature show that selective breeding with inbreeding control is likely the best strategy for genetic improvement of most molluscs, and on average growth rate can be improved by 10% per generation and disease resistance by 15% per generation across the major farmed species by implementing individual or family-based selection. Rapid advances in sequencing technology have resulted in a wealth of genomic resources for key species with the potential to greatly improve hatchery-based selective breeding of molluscs. In this review, we catalog the range of genomic resources currently available for molluscs of aquaculture interest and discuss the bottlenecks, including lack of high-quality reference genomes and the relatively high cost of genotyping, as well as opportunities for applying genomics-based selection.

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Section: Opportunities For Genomics-based Selectionmentioning

confidence: 99%

Genomic Tools and Selective Breeding in Molluscs

Hollenbeck

Johnston

2018

Front. Genet.

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“…High-density (HD) genetic maps provide information on genome organisation by establishing the cartography of thousands of markers, which can aid to disentangle the genetic architecture of productive or evolutionary traits. Moreover, these maps represent an essential tool for comparative genomics and can facilitate whole genome assembly 2 , 3 . The advent of next generation sequencing (NGS) has dramatically reduced the cost and time required for genomic analysis, 4 , 5 thus contributing to a fast increase of genomic resources.…”

Section: Introductionmentioning

confidence: 99%

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

Maroso¹,

Hermida

Millán³

et al. 2018

DNA Research

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Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.

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“…Recent advances in GBS technology have allowed the identification of numerous genetic molecular markers at a reasonable cost. This has promoted the development of several high-throughput single-nucleotide polymorphism (SNP) genotyping methods [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color (Psc) in hulless barley

Yao

et al. 2018

Hereditas

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BackgroundColored hulless barley are more suitable in food processing compared to normal (yellow) varieties because it is rich in bioactive compounds and produces higher extraction pearling fractions. Therefore, seed coat color is an important agronomic trait for the breeding and study of hulless barley.ResultsGenotyping-by-sequencing single-nucleotide polymorphism (GBS-SNP) analysis of a doubled haploid (DH) mapping population (Nierumuzha × Kunlun10) was conducted to map the purple seed coat color genes (Psc). A high-density genetic map of hulless barley was constructed, which contains 3662 efficient SNP markers with 1129 bin markers. Seven linkage groups were resolved, which had a total length of 645.56 cM. Chromosome length ranged from 60.21 cM to 127.21 cM, with average marker density of 0.57 cM. A total of five loci accounting for 3.79% to 23.86% of the observed phenotypic variation for Psc were detected using this high-density map. Five structural candidate genes (F3’M, HID, UF3GT, UFGT and 5MAT) and one regulatory factor (Ant1) related to flavonoid or anthocyanin biosynthesis were identified..ConclusionsFive structural candidate genes and one regulatory factor related to flavonoid or anthocyanin biosynthesis have been identified using a high-density genetic map of hulless barley. This study lays the foundation for map-based cloning of Psc but provides a valuable tool for studying marker-trait associations and its application to marker-assisted breeding of hulless barley.Electronic supplementary materialThe online version of this article (10.1186/s41065-018-0072-6) contains supplementary material, which is available to authorized users.

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Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Manila clam Ruditapes philippinarum

Cited by 30 publications

References 54 publications

Genomic Tools and Selective Breeding in Molluscs

Genomic Tools and Selective Breeding in Molluscs

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color (Psc) in hulless barley

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