Data and Code from: Association studies of salinity tolerance in sunflower provide robust breeding and selection strategies under climate change

Abstract
Phytotoxic soil salinity is a global problem, and in the northern Great Plains and western Canada, salt accumulates on the surface of marine sediment soils with high water tables under annual crop cover, particularly near wetlands. Crop production can overcome saline-affected soils using crop species and cultivars with salinity tolerance along with changes in management practices. This research seeks to improve our understanding of sunflower (Helianthus annuus) genetic tolerance to high salinity soils. Genome-wide association was conducted using the Sunflower Association Mapping panel grown for two years in naturally occurring saline soils (2016 and 2017, near Indian Head, Saskatchewan, Canada), and six phenotypes were measured: days to bloom, height, leaf area, leaf mass, oil percentage, and yield. Plot level soil salinity was determined by grid sampling of soil followed by kriging. Three estimates of sunflower performance were calculated: 1) under low soil salinity ( 4 dS/m), and 3) plasticity (regression coefficient between phenotype and soil salinity). Fourteen loci were significant, with one instance of co-localization between a leaf area and a leaf mass locus. Some genomic regions identified as significant in this study were also significant in a recent greenhouse salinity experiment using the same panel. Also, some candidate genes underlying significant QTL have been identified in other plant species as having a role in salinity response. This research identifies alleles for cultivar improvement and for genetic studies to further elucidate salinity tolerance pathways.
Contents
 This link to GitHub contains the data and analysis scripts used in this research, including R analysis scripts, and data analyzed.

摘要
植物毒害土壤盐渍化是全球性问题，尤其是在北美大平原和加拿大西部，盐分在具有高地下水位的海相沉积土壤表层累积，尤其在湿地附近。通过采用耐盐性作物品种以及调整管理措施，作物生产可以克服盐渍化土壤的影响。本研究旨在深化我们对向日葵（Helianthus annuus）对高盐土壤遗传耐性的理解。利用在自然发生的盐渍土壤中连续种植两年（2016年和2017年，加拿大萨斯喀彻温省印第安头镇附近）的向日葵关联图谱，进行了全基因组关联分析，并测量了六个表型指标：开花天数、高度、叶面积、叶片质量、油分百分比和产量。通过网格采样土壤并随后进行克里金插值，确定了地块级别的土壤盐分。计算了三个向日葵性能估计值：1）在低土壤盐分条件下（4 dS/m），3）塑性（表型与土壤盐分之间的回归系数）。十四个位点表现出显著性，其中叶面积位点和叶片质量位点存在一个共定位实例。本研究中确定的某些显著基因组区域，在近期使用同一图谱进行温室盐渍实验中也被证实具有显著性。此外，一些候选基因在其它植物物种中被发现，其在盐分响应中扮演着角色。本研究识别了用于品种改良和遗传研究的等位基因，以进一步阐明耐盐性途径。
内容
此GitHub链接包含用于本研究的所有数据和分析脚本，包括R分析脚本和分析数据。