SMRT-AgRenSeq-d in potato (Solanum tuberosum) identifies candidates for the nematode resistance Gpa5
SMRT-AgRenSeq-d in potato (Solanum tuberosum) identifies candidates for the nematode resistance Gpa5
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马铃薯（Solanum tuberosum）中的 SMRT-AgRenSeq-d 鉴定了线虫抗性 Gpa5 的候选者
DOI：
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
I. Hein
中科院分区：
文献类型：
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作者：
Yuhan Wang;Lynn H Brown;T. Adams;Yuk Woon Cheung;Jie Li;V. Young;D. Todd;M. Armstrong;Konrad Neugebauer;A. Kaur;B. Harrower;S. Oome;Xiaodan Wang;M. Bayer;I. Hein
马铃薯是世界上第三大粮食作物。多种病原体威胁着可持续的作物生产，但在许多情况下，可以通过部署属于核苷酸结合、富含亮氨酸重复序列（NLR）基因家族的抗病基因来控制。为了在已建立的品种中鉴定功能性NLR，我们已经成功地在四倍体马铃薯中建立了SMRT-AgRenSeq，并且通过在我们称为SMRT-AgRenSeq-d的方法中包括dRenSeq来进一步增强该方法。包含dRenSeq使得能够在关联分析之后通过建立跨抗性和易感马铃薯的存在/不存在矩阵来过滤候选物，所述存在/不存在矩阵被转换成F1分数。使用来自栽培品种Innovator的NLRome的基于SMRT-RenSeq的序列表示，SMRT-AgRenSeq-d分析可靠地鉴定了具有可变表型穿透的117个品种的组中的晚疫病抗性基准基因R1、R2-like、R3 a和R3 b。所有基准基因均以1的F1评分鉴定，这表明该组中的绝对连锁。当应用于控制马铃薯胞囊线虫（PCN）物种Globodera pallida（致病型Pa 2/3）的难以捉摸的线虫病抗性基因Gpa 5时，SMRT-AgRenSeq-d鉴定了9个强有力的候选者。这些映射到马铃薯5号染色体上先前确定的位置，并且是晚疫病抗性基因R1的潜在同源物。假设NLR参与控制许多类型的抗性，SMRT-AgRenSeq-d可以容易地应用于不同的作物和病原体系统。例如，在马铃薯中，SMRT-AgRenSeq-d有助于进一步研究存在表型数据的难以捉摸的PCN抗性H1或H3。
Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify functional NLRs in established varieties, we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMRT-AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible potatoes that is translated into an F1 score. Using a SMRT-RenSeq based sequence representation of the NLRome from the cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes R1, R2-like, R3a and R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1 which indicates absolute linkage in the panel. When applied to the elusive nematode disease resistance gene Gpa5 that controls the Potato Cyst Nematode (PCN) species Globodera pallida (pathotypes Pa2/3), SMRT-AgRenSeq-d identified nine strong candidates. These map to the previously established position on potato chromosome 5 and are potential homologs of the late blight resistance gene R1. Assuming that NLRs are involved in controlling many types of resistances, SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems. In potato, SMRT-AgRenSeq-d lends itself, for example, to further study the elusive PCN resistances H1 or H3 for which phenotypic data exist.
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影响因子：
64.5
作者：
Van de Weyer, Anna-Lena;Monteiro, Freddy;Bemm, Felix
通讯作者：
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DOI：
10.1101/2022.11.01.514708
发表时间：
2022
期刊：
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影响因子：
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作者：
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通讯作者：
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DOI：
10.1101/360644
发表时间：
2018
期刊：
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影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
ALTSCHUL, SF;GISH, W;LIPMAN, DJ
通讯作者：
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