Whole genome resequencing of pink stem borer (Part 2/4)

Understanding the genetic basis of adaptive evolution following habitat
expansion can have important implications for pest
management. The pink stem borer (PSB), Sesamia inferens
(Walker), is a destructive pest of rice that was historically restricted
to regions south of N34° latitude in China. However, with changes in
global climate and farming practices, the distribution of this moth has
progressively exceeded its traditional limit of 34° N and encompassed most
regions in North China. However, the evolutionary processes and local
adaptative changes of this species, are not yet fully
understood. Here, we employed genome resequencing to genotype
over 1 million of high‐quality SNPs and 20,000 SVs from 14 geographical
populations across China. Three highly differentiated genetic groups were
formed, corresponding to Northern and Southern China regions and the
Yunnan-Guizhou Plateau. The pairwise genetic distance between locations
was highly correlated with geographic and environmental distance. Our
estimates of evolutionary history indicate asymmetric migration with
varying population sizes across three genetic groups. Selective sweep
analyses highlight the strongly selected insect cuticle GRP genes enhanced
desiccation adaptability of the northern group and SETMAR gene associated
with range expansion and local adaptation in the Shandong population.
Based on an integrated analysis of transcriptome and enGWAS, we also
identified the CYP321A7 gene as being involved in the PSB
adaption to desiccation climates. Our findings revealed the
phylogeography, demographic dynamics and evolutionary forces of PSB and
identified potential candidate genes to explore the genetic adaptation to
novel environments, which have significant implications for the
development of effective strategies to control this pest.

解析栖息地扩张过程中适应性演化的遗传基础，对害虫防控具有重要意义。粉红色茎螟（pink stem borer, PSB），学名*Sesamia inferens*（Walker），是一种水稻重大害虫，历史上其分布仅局限于中国北纬34°以南区域。然而，随着全球气候变化与耕作模式的改变，该蛾类的分布范围已逐步突破北纬34°的传统界限，覆盖了中国华北大部分区域。但目前学界对该物种的演化过程与本地适应性变化仍缺乏充分认知。本研究采用基因组重测序技术，对中国境内14个地理种群的逾100万个高质量单核苷酸多态性（single nucleotide polymorphism, SNP）与2万个结构变异（structural variation, SV）进行基因分型。分析显示种群可划分为3个高度分化的遗传类群，分别对应中国北方、南方区域以及云贵高原。种群间的两两遗传距离与地理距离及环境距离均呈显著相关。演化历史重建结果表明，3个遗传类群间存在不对称的基因流，且各类群的种群规模存在差异。选择性清除分析显示，受强烈正向选择的昆虫表皮糖蛋白（glycine-rich protein, GRP）基因提升了北方类群的耐旱适应性；而SETMAR基因与山东种群的分布扩张及本地适应性相关。本研究结合转录组与全环境关联分析（environment-wide association study, enGWAS）的整合分析，进一步鉴定出CYP321A7基因参与粉红色茎螟对干旱气候的适应性调控。本研究阐明了粉红色茎螟的系统地理学格局、种群动态历史与演化驱动力，并鉴定出若干参与新环境适应性的潜在候选基因，为研发该害虫的高效防控策略提供了重要理论依据。