当前位置: X-MOL 学术Genome Biol. Evol. › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Co-expression clusters and allele-specific expression in metabolism-based herbicide resistance.
Genome Biology and Evolution ( IF 3.3 ) Pub Date : 2020-09-11 , DOI: 10.1093/gbe/evaa191
Darci A Giacomini 1 , Eric L Patterson 2 , Anita Küpper 3 , Roland Beffa 3 , Todd A Gaines 4 , Patrick J Tranel 1
Affiliation  

In the last decade, Amaranthus tuberculatus has evolved resistance to 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors in multiple states across the midwestern US. Two populations resistant to both mode-of-action groups, one from Nebraska (NEB) and one from Illinois (CHR), were studied using an RNA-seq approach on F2 mapping populations to identify the genes responsible for resistance. Using both an A. tuberculatus transcriptome assembly and a high-quality grain amaranth (A. hypochondriacus) genome as references, differential transcript and gene expression analyses were conducted to identify genes that were significantly over- or under-expressed in resistant plants. When these differentially expressed genes (DEGs) were mapped on the A. hypochondriacus genome, physical clustering of the DEGs was apparent along several of the 16 A. hypochondriacus scaffolds. Furthermore, single-nucleotide polymorphism (SNP) calling to look for resistant-specific (R) variants, and subsequent mapping of these variants, also found similar patterns of clustering. Specifically, regions biased towards R alleles overlapped with the DEG clusters. Within one of these clusters, allele-specific expression of cytochrome P450 81E8 was observed for 2,4-D resistance in both the CHR and NEB populations, and phylogenetic analysis indicated a common evolutionary origin of this R allele in the two populations.

中文翻译:

基于代谢的除草剂抗性中的共表达簇和等位基因特异性表达。

在过去十年中,Amaranthus tuberculatus在美国中西部的多个州对 2,4-二氯苯氧乙酸 (2,4-D) 和 4-羟基苯丙酮酸双加氧酶 (HPPD) 抑制剂产生了抗药性。使用 RNA-seq 方法对 F 2作图群体进行研究,以鉴定导致抗性的基因,研究了对两种作用方式组均具有抗性的两个群体,一个来自内布拉斯加州 (NEB),另一个来自伊利诺伊州 (CHR) 。使用A. tuberculatus转录组组装和优质谷粒苋(A. hypochondriacus) 基因组作为参考,进行差异转录和基因表达分析以鉴定在抗性植物中显着过表达或表达不足的基因。当这些差异表达基因 (DEGs) 被定位到A. hypochondriacus基因组上时,DEGs 的物理聚类沿着 16 个A. hypochondriacus 中的几个很明显脚手架。此外,单核苷酸多态性 (SNP) 调用寻找抗性特异性 (R) 变体,以及这些变体的后续映射,也发现了类似的聚类模式。具体而言,偏向 R 等位基因的区域与 DEG 簇重叠。在这些簇之一中,在 CHR 和 NEB 种群中观察到细胞色素 P450 81E8 的等位基因特异性表达,用于 2,4-D 抗性,并且系统发育分析表明该 R 等位基因在这两个种群中具有共同的进化起源。
更新日期:2020-09-12
down
wechat
bug