Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat.
Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat.
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DOI：
10.1111/tpj.13204
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发表时间：
2016-08
期刊：
影响因子：
--
通讯作者：
Hall A
中科院分区：
文献类型：
--
作者：
Gardiner LJ;Bansept-Basler P;Olohan L;Joynson R;Brenchley R;Hall N;O'Sullivan DM;Hall A
以前，我们通过将其与序列捕获相结合并将序列数据映射到使用小麦-短柄草同线性组织的假染色体来扩展测序映射的实用性。这一点，与定制的单倍型算法，使我们能够映射开花时间在二倍体小麦一粒小麦L。鉴定一组缺失的基因（加德纳等人，2014年）。在这里，我们开发了基因富集和滑动窗口同线性映射分析的组合，以映射六倍体小麦黄条锈抗性的Yr 6基因座。使用110 MB NimbleGen捕获探针组来富集和测序源自Avalon和Cadenza杂交的六倍体小麦的加倍单倍体作图群体。通过使用定制的管道和算法定位到POPSEQ染色体假分子来鉴定Yr 6基因座（Chapman等人，2015年）。此外，使用新开发的假染色体序列作为作图参考鉴定了相同的基因座，所述序列基于用于序列富集的基因序列。伪染色体使我们能够证明测序定位的应用，即使是不明确的多倍体基因组，其中染色体是不完整的，亚基因组组装崩溃。这项分析独特地使我们能够：比较小麦基因组注释;识别Yr 6位点-定义比以前可能的更小的基因区域;将间隔与一个小麦亚基因组相关联并增加相关SNP标记的密度。最后，我们在iPlant中构建了管道，使其成为用于表型映射的用户友好社区资源。将测序管道应用于大型多倍体基因组（如六倍体小麦）具有挑战性。在这里，我们提出了一种方法，负责表型的基因的快速定位，并证明其实用性，通过定位抗病基因。我们表明，我们在iPlant上提供的定制测序映射管道可以应用于定义不明确的多倍体基因组。
Previously we extended the utility of mapping‐by‐sequencing by combining it with sequence capture and mapping sequence data to pseudo‐chromosomes that were organized using wheat–Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping‐by‐synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo‐chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo‐chromosomes allow us to demonstrate the application of mapping‐by‐sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub‐genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus – defining a smaller genic region than was previously possible; associate the interval with one wheat sub‐genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user‐friendly community resource for phenotype mapping. It is challenging to apply mapping‐by‐sequencing pipelines to large polyploid genomes such as hexaploid wheat. Here we present a method for the rapid mapping of genes responsible for a phenotype, and demonstrate its utility by mapping a disease resistance gene. We show that our bespoke mapping‐by‐sequencing pipeline, available on iPlant, can be applied to poorly defined polyploid genomes.
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影响因子：
4.5
作者：
Chen, XM;Moore, M;Jackson, L
通讯作者：
Jackson, L
DOI：
10.1534/g3.114.012963
发表时间：
2014-09-18
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Mackay IJ;Bansept-Basler P;Barber T;Bentley AR;Cockram J;Gosman N;Greenland AJ;Horsnell R;Howells R;O'Sullivan DM;Rose GA;Howell PJ
通讯作者：
Howell PJ
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
5.6
作者：
Goff SA;Vaughn M;McKay S;Lyons E;Stapleton AE;Gessler D;Matasci N;Wang L;Hanlon M;Lenards A;Muir A;Merchant N;Lowry S;Mock S;Helmke M;Kubach A;Narro M;Hopkins N;Micklos D;Hilgert U;Gonzales M;Jordan C;Skidmore E;Dooley R;Cazes J;McLay R;Lu Z;Pasternak S;Koesterke L;Piel WH;Grene R;Noutsos C;Gendler K;Feng X;Tang C;Lent M;Kim SJ;Kvilekval K;Manjunath BS;Tannen V;Stamatakis A;Sanderson M;Welch SM;Cranston KA;Soltis P;Soltis D;O'Meara B;Ane C;Brutnell T;Kleibenstein DJ;White JW;Leebens-Mack J;Donoghue MJ;Spalding EP;Vision TJ;Myers CR;Lowenthal D;Enquist BJ;Boyle B;Akoglu A;Andrews G;Ram S;Ware D;Stein L;Stanzione D
通讯作者：
Stanzione D
影响因子：
7.2
作者：
Austin, Ryan S.;Vidaurre, Danielle;Guttman, David S.
通讯作者：
Guttman, David S.