Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton.
Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton.
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DOI：
10.1186/s12864-016-2605-6
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发表时间：
2016-04-19
期刊：
影响因子：
4.4
通讯作者：
Zhang Z
中科院分区：
文献类型：
--
作者：
Liu D;Zhang J;Liu X;Wang W;Liu D;Teng Z;Fang X;Tan Z;Tang S;Yang J;Zhong J;Zhang Z
由于对棉花品质性状的分子基础了解甚少，提高棉花品质是棉花育种面临的主要挑战。控制棉纤维品质性状的数量性状位点（QTL）精细定位和候选基因预测有助于阐明棉纤维品质的分子基础。在我们之前的研究中，在陆地棉6号染色体T1位点附近发现了一个控制多个纤维品质性状的主要QTL。为了精细定位这一主要QTL，从重组自交系群体（T586 × Yumian 1）中选择重组自交系（RIL118）与Yumian 1号杂交，建立了F2群体，共6975个个体。QTL定位于标记HAU2119和SWU2302之间0.28 cm的区间。QTL解释了54.7% （LOD = 222.3）、40.5% （LOD = 145.0）、50.0% （LOD = 194.3）和30.1% （LOD = 100.4）的表型变异，纤维长度、马克隆、强度和均匀度的加性效应分别为2.78、- 0.43、2.92和1.90个单位。该QTL区域在雷蒙地鼠基因组序列第10号染色体上对应2.7 mb的区间，在毛鼠基因组序列第A06号染色体上对应5.3 mb的区间。玉棉1号的纤维长度较RIL118长，从3 DPA到7 DPA不等。育棉1号和RIL118的胚珠0 DPA和纤维5 DPA的RNA-Seq结果显示，雷蒙地弓形虫基因组QTL区有4个基因存在极显著差异表达。RT-PCR分析结果显示，毛藓基因组QTL区有3个基因表现相似。本研究将影响4个纤维品质性状的主要QTL定位在0.28 cm区间，并通过RNA-Seq和RT-PCR分析鉴定出3个候选基因。精细定位和RNA-Seq的结合是在大基因组中发现QTL候选者的有力策略。本文的在线版本（doi:10.1186/s12864-016-2605-6）包含补充材料，可供授权用户使用。
Improving fiber quality is a major challenge in cotton breeding, since the molecular basis of fiber quality traits is poorly understood. Fine mapping and candidate gene prediction of quantitative trait loci (QTL) controlling cotton fiber quality traits can help to elucidate the molecular basis of fiber quality. In our previous studies, one major QTL controlling multiple fiber quality traits was identified near the T1 locus on chromosome 6 in Upland cotton. To finely map this major QTL, the F2 population with 6975 individuals was established from a cross between Yumian 1 and a recombinant inbred line (RIL118) selected from a recombinant inbred line population (T586 × Yumian 1). The QTL was mapped to a 0.28-cM interval between markers HAU2119 and SWU2302. The QTL explained 54.7 % (LOD = 222.3), 40.5 % (LOD = 145.0), 50.0 % (LOD = 194.3) and 30.1 % (LOD = 100.4) of phenotypic variation with additive effects of 2.78, −0.43, 2.92 and 1.90 units for fiber length, micronaire, strength and uniformity, respectively. The QTL region corresponded to a 2.7-Mb interval on chromosome 10 in the G. raimondii genome sequence and a 5.3-Mb interval on chromosome A06 in G. hirsutum. The fiber of Yumian 1 was much longer than that of RIL118 from 3 DPA to 7 DPA. RNA-Seq of ovules at 0 DPA and fibers at 5 DPA from Yumian 1 and RIL118 showed four genes in the QTL region of the G. raimondii genome to be extremely differentially expressed. RT-PCR analysis showed three genes in the QTL region of the G. hirsutum genome to behave similarly. This study mapped a major QTL influencing four fiber quality traits to a 0.28-cM interval and identified three candidate genes by RNA-Seq and RT-PCR analysis. Integration of fine mapping and RNA-Seq is a powerful strategy to uncover candidates for QTL in large genomes. The online version of this article (doi:10.1186/s12864-016-2605-6) contains supplementary material, which is available to authorized users.