Combining genomic selection with genome-wide association analysis identified a large-effect QTL and improved selection for red rot resistance in sugarcane

文献类型： 外文期刊

第一作者： O'Connell, Anthony

作者： O'Connell, Anthony;Deo, Jasmin;Deomano, Emily;Wei, Xianming;Lakshmanan, Prakash;Jackson, Phillip;Aitken, Karen S. S.;Manimekalai, Ramaswamy;Mohanraj, Krishnasamy;Hemaprabha, Govinda;Ram, Bakshi;Viswanathan, Rasappa;Lakshmanan, Prakash;Lakshmanan, Prakash;Lakshmanan, Prakash

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关键词： sugarcane; GWAS; genome wide association study; red rot; molecular breeding; genomic selection

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：6.627； 五年影响因子：7.255 ）

ISSN： 1664-462X

年卷期： 2022 年 13 卷

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收录情况： SCI

摘要： Red rot caused by the fungus Colletotrichum falcatum is the main disease limiting sugarcane productivity in several countries including the major producer India. The genetic basis for red rot resistance is unclear. We studied a panel of 305 sugarcane clones from the Australian breeding program for disease response phenotype and genotype using an Affymetrix (R) Axiom (R) array, to better understand the genetic basis of red rot resistance. SNP markers highly significantly associated with red rot response (<= 10(-8)) were identified. Markers with largest effect were located in a single 14.6 Mb genomic region of sorghum (the closest diploid relative of sugarcane with a sequenced genome) suggesting the presence of a major-effect QTL. By genomic selection, the estimated selection accuracy was similar to 0.42 for red rot resistance. This was increased to similar to 0.5 with the addition of 29 highly significant SNPs as fixed effects. Analysis of genes nearby the markers linked to the QTL revealed many biotic stress responsive genes within this QTL, with the most significant SNP co-locating with a cluster of four chitinase A genes. The SNP markers identified here could be used to predict red rot resistance with high accuracy at any stage in the sugarcane breeding program.

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