利用 PotatoMASH 扩增子测序发现二倍体马铃薯克隆中农艺和品质性状的 QTL。

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY
Lea Vexler, Maria de la O Leyva-Perez, Agnieszka Konkolewska, Corentin R Clot, Stephen Byrne, Denis Griffin, Tom Ruttink, Ronald C B Hutten, Christel Engelen, Richard G F Visser, Vanessa Prigge, Silke Wagener, Gisele Lairy-Joly, Jan-David Driesprong, Ea Høegh Riis Sundmark, A Nico O Rookmaker, Herman J van Eck, Dan Milbourne
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引用次数: 0

摘要

我们对来自西北欧六个独立马铃薯育种计划的618个二倍体马铃薯克隆群体进行了基因分型。利用标准化方案和普通对照品种对二倍体的23个性状进行了表型分析,使我们能够得出大多数性状的全群体估计值。随后,我们进行了全基因组关联研究(GWAS),利用SNPs和从回读相位中得到的短读单倍型确定了所有性状的数量性状位点(QTL)。在这项研究中,我们使用了一个名为 PotatoMASH(马铃薯多单倍型扫描单倍型)的标记平台;这是一种基于集合多重扩增子测序的方法。通过这种方法,可以将一个扩增片段内的相邻 SNP 结合起来,生成多等位基因短读数单倍型(haplotags),从而捕捉组成 SNP 之间的重组历史,并以不同于单个双等位基因 SNP 的方式反映特定位点的等位基因多样性。我们在两种标记类型中总共发现了 37 个独特的 QTL。利用 SNP 和单倍标记检测到了 10 个 QTL 核心。单体标记还能检测出 14 个基于 SNP 集未发现的 QTL。相反,双等位 SNP 组也发现了 13 个使用单体标记组无法检测到的 QTL。我们的结论是,两种标记类型应常规并行使用,以最大限度地提高 QTL 的检测能力。我们报告了九个性状的 19 个新 QTL:表皮光滑度、萌芽休眠期、总块茎数、块茎长度、产量、崩裂色、烹饪后发黑、烹饪类型和眼深。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
QTL discovery for agronomic and quality traits in diploid potato clones using PotatoMASH amplicon sequencing.

We genotyped a population of 618 diploid potato clones derived from six independent potato-breeding programmes from NW-Europe. The diploids were phenotyped for 23 traits, using standardized protocols and common check varieties, enabling us to derive whole population estimators for most traits. We subsequently performed a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) for all traits with SNPs and short-read haplotypes derived from read-backed phasing. In this study, we used a marker platform called PotatoMASH (Potato Multi-Allele Scanning Haplotags); a pooled multiplex amplicon sequencing based approach. Through this method, neighboring SNPs within an amplicon can be combined to generate multiallelic short-read haplotypes (haplotags) that capture recombination history between the constituent SNPs and reflect the allelic diversity of a given locus in a different way than single bi-allelic SNPs. We found a total of 37 unique QTL across both marker types. A core of 10 QTL was detected with SNPs as well as with haplotags. Haplotags allowed to detect an additional 14 QTL not found based on the SNP set. Conversely, the bi-allelic SNP set also found 13 QTL not detectable using the haplotag set. We conclude that both marker types should routinely be used in parallel to maximize the QTL detection power. We report 19 novel QTL for nine traits: Skin Smoothness, Sprout Dormancy, Total Tuber Number, Tuber Length, Yield, Chipping Color, After-cooking Blackening, Cooking Type, and Eye depth.

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来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
期刊介绍: G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.
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