Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.).
Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.).
复制标题
使用甘蔗（甘蔗属）中的高密度遗传图谱和批量分离 RNA 测序进行定量性状基因座作图和 KASP 标记黑穗病筛选测定的开发
DOI：
10.3389/fpls.2021.796189
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发表时间：
2021
影响因子：
5.6
通讯作者：
Duan W
中科院分区：
文献类型：
--
作者：
Gao Y;Zhou S;Huang Y;Zhang B;Xu Y;Zhang G;Lakshmanan P;Yang R;Zhou H;Huang D;Liu J;Tan H;He W;Yang C;Duan W
甘蔗是全球最重要的经济作物之一。它是生物乙醇的第二大来源，也是全球生物质发电和制糖的主要作物。甘蔗黑穗病是甘蔗生产中的一种主要病害，由甘蔗黑穗病孢菌引起，目前主要采用抗黑穗病品种进行防治。在中国，黑穗病仍然是甘蔗生产的最大制约因素，因此影响了甘蔗作为能源原料的价值。与黑穗病抗性相关的数量性状位点和连锁诊断标记是抗黑穗病育种的重要工具。在这里，我们开发了一个F1群体（192个后代），通过杂交两个甘蔗品种具有对比黑穗病抗性，并用于全基因组单核苷酸多态性（SNP）的发现和定位，使用高通量基因分型方法称为“特定位点扩增片段测序（SLAF-seq）和bulked-segregant RNA测序（BSR-seq）。SLAF-seq产生了148，500个多态性SNP标记。利用SNP和先前鉴定的SSR标记，产生了平均1.96 cM标记间隔的综合遗传图谱。利用该遗传图谱和4个年份F1代的抗黑穗病性评分，共定位到21个主效QTL，表型方差解释率（PVE）> 8.0%。其中10个QTL稳定（可重复），变异系数在8.0 ~ 81.7%之间。BSR-seq分析检测到4个QTL。将主效QTL与甘蔗祖先割手密的基因组进行比对，发现6个标记共定位。QTL标记和BSR-seq单基因功能注释有助于鉴定位于主效QTL的4个抗病候选基因。将77个来自主效QTL的SNPs转化为竞争性等位基因特异性PCR（KASP）标记，其中5个与黑穗病抗性极显著连锁。本研究所发现的共定位QTL、候选抗病基因和KASP标记为甘蔗抗黑穗病分子标记辅助育种提供了实用的工具。
Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called “specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.
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影响因子：
3.2
作者：
CHAO, CP;HOY, JW;MARTIN, FA
通讯作者：
MARTIN, FA
影响因子：
5.4
作者：
Debibakas, S.;Rocher, S.;Garsmeur, O.;Toubi, L.;Roques, D.;D'Hont, A.;Hoarau, J. -Y.;Daugrois, J. H.
通讯作者：
Daugrois, J. H.
影响因子：
7
作者：
Hill JT;Demarest BL;Bisgrove BW;Gorsi B;Su YC;Yost HJ
通讯作者：
Yost HJ
影响因子：
5.2
作者：
Cordeiro, GM;Taylor, GO;Henry, RJ
通讯作者：
Henry, RJ
影响因子：
3.7
作者：
Elshire RJ;Glaubitz JC;Sun Q;Poland JA;Kawamoto K;Buckler ES;Mitchell SE
通讯作者：
Mitchell SE