A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton.
A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton.
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DOI：
10.1186/s12864-016-3249-2
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发表时间：
2016-11-09
期刊：
影响因子：
4.4
通讯作者：
Fang DD
中科院分区：
文献类型：
--
作者：
Islam MS;Thyssen GN;Jenkins JN;Zeng L;Delhom CD;McCarty JC;Deng DD;Hinchliffe DJ;Jones DC;Fang DD
棉花为全球纺织业提供了绝大多数天然纤维。产量和纤维品质之间的负相关性阻碍了育种者同时改善这些性状的能力。通过多个不同亲本的随机交配而形成的多亲本高世代互交（MAGIC）群体具有打破这种负相关的能力。测序基因分型（GBS）是一种可以快速鉴定和分型大量单核苷酸多态性（SNP）的方法。使用GBS技术对MAGIC群体进行基因分型将使我们能够以高分辨率识别标记-性状关联。通过对11个棉花品种的5代随机交配，构建了高地棉MAGIC群体。在这项研究中，纤维品质数据从四个环境和6071 SNP标记产生的GBS和223微卫星标记的547重组自交系（RILs）的MAGIC人口进行全基因组关联研究（GWAS）。通过采用混合线性模型，GWAS使我们能够识别标记显着相关的纤维数量性状位点（QTL）。我们在A07染色体上鉴定并验证了一个与4个纤维品质性状[短纤维含量（SFC）、比强度（STR）、长度（UHM）和整齐度（UI）]相关的QTL簇。我们进一步确定了该区域中与纤维品质属性相关的候选基因。基因表达和氨基酸替换分析表明，再生鳞茎生物发生1（GhRBB1_A07）基因是高地棉上级纤维品质的候选基因。从阿卡拉Ultima中GhRBB1_A07编码序列中的18 bp缺失设计的DNA标记CFBid 0004与MAGIC RILs和105个另外的商业高地棉花品种中纤维品质的改善相关。使用GBS和MAGIC群体可以更精确地定位高地棉纤维QTL。本研究所鉴定的纤维品质QTL及其相关标记可用于棉花育种中的标记辅助选择或基因组选择。通过生物技术或基因编辑对GhRBB1_A07基因进行靶向操作可能会潜在地改善棉花纤维品质。本文的在线版本（doi：10.1186/s12864-016-3249-2）包含补充材料，可供授权用户使用。
Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders’ ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP). Genotyping a MAGIC population using GBS technologies will enable us to identify marker-trait associations with high resolution. An Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By employing a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits [short fiber content (SFC), strength (STR), length (UHM) and uniformity (UI)] on chromosome A07. We further identified candidate genes related to fiber quality attributes in this region. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars. Using GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection or genomic selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality. The online version of this article (doi:10.1186/s12864-016-3249-2) contains supplementary material, which is available to authorized users.
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影响因子：
4.4
作者：
Kim HJ;Tang Y;Moon HS;Delhom CD;Fang DD
通讯作者：
Fang DD
影响因子：
4.4
作者：
Fang DD;Jenkins JN;Deng DD;McCarty JC;Li P;Wu J
通讯作者：
Wu J
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
DOI：
10.1186/1939-8433-6-11
发表时间：
2013-05-06
期刊：
Rice (New York, N.Y.)
影响因子：
--
作者：
Bandillo N;Raghavan C;Muyco PA;Sevilla MA;Lobina IT;Dilla-Ermita CJ;Tung CW;McCouch S;Thomson M;Mauleon R;Singh RK;Gregorio G;Redoña E;Leung H
通讯作者：
Leung H
影响因子：
3.7
作者：
Kim HJ;Hinchliffe DJ;Triplett BA;Chen ZJ;Stelly DM;Yeater KM;Moon HS;Gilbert MK;Thyssen GN;Turley RB;Fang DD
通讯作者：
Fang DD