SNP alleles for pooled DNA samples of Vicia villosa targeting QTL for pod dehiscence and seed dormancy

Hairy vetch (Vicia villosa Roth) is a promising legume cover crop, but its use is limited by high rates of pod dehiscence and seed dormancy.  We used phenotypically contrasting pooled DNA samples (n=24 with 29-74 individuals per sample) from an ongoing cover crop breeding program across four environments (site-year combinations: Maryland 2020, Maryland 2022, Wisconsin 2021, Wisconsin 2022) to find genetic associations and genomic prediction accuracies for pod dehiscence and seed dormancy. We also combined pooled DNA sample genetic association results with the results of a prior genome-wide association study. Genomic prediction resulted in positive predictive abilities for both traits between environments and with an independent dataset (0.34-0.50), but reduced predictive ability for DNA pools with divergent seed dormancy in the Maryland environments (0.07-0.15). The pooled DNA samples found six significant (false discovery rate q-value<0.01) quantitative trait loci (QTL) for seed dor..., This study sampled individuals evaluated during ongoing breeding efforts of the Cover Crop Breeding Network.  Four environments were selected which had sufficient population size and contained meaningful variability in pod dehiscence and seed dormancy.  For the remainder of this study, I will refer to each environment using an abbreviation and final two digits of the harvest year (i.e. Beltsville, MD 2020 and 2022: 20MD, 22MD, Prairie du Sac, WI 2021 and 2022: 21WI and 22WI). The 20MD breeding nursery was planted on Sept 27th 2019 (39°01′50″ N, 76°55′59″ W, Russett–Christiana complex soil) into a tilled field which was broadcast seeded with turf red fescue (Festuca rubra L.; 340 kg ha-1).  On November 5th 2019, 20MD was sprayed with Raptor (ammonium salt of imazamox; 0.37 L ha−1) to control winter weeds. For 20MD, pods were collected from June 23rd 2020 to June 30th 2020 (harvest varies with pod maturity of individual genotypes, see below).  The 22MD nursery was planted at the same loca..., , # SNP alleles for pooled DNA samples of Vicia villosa targeting QTL for pod dehiscence and seed dormancy

## Description of the data and file structure

VetchPoolDNA_MarkerInformation.csv contains columns indicating the reference and alternate alleles for each SNP. It also indicates the percent individuals with missing date in the individual sequencing dataset for that SNP. Similarly, there is a column with the mean read depth within the sequencing of pooled DNA.

VetchPoolDNA_Dosage.csv contains allele dosages with columns representing sites and rows representing individuals or DNA pools (ID column). 99 indicates missing data. Pool allele frequencies are the mean allele read frequency! Therefore, these are on different scales (individuals 0-2 and DNA pools 0-1).

VetchPoolDNA_Performance.csv contains the pod dehiscence rates, seed dormancy rates, and number of individuals with phenotypic information included in each pool.

## Sharing/Access information

Individuals in this file ...

毛叶苕子（Vicia villosa Roth）是一种极具应用前景的豆科覆盖作物，但其应用受限于较高的裂荚率与种子休眠性。本研究利用来自一项正在进行的覆盖作物育种项目、在四个环境（地点-年份组合：马里兰州2020、马里兰州2022、威斯康星州2021、威斯康星州2022）中表型差异显著的混合DNA样本（每组样本包含29-74个个体，共24组），旨在解析裂荚率与种子休眠性的遗传关联并评估基因组预测精度。我们还将混合DNA样本的遗传关联分析结果与此前的全基因组关联研究（Genome-Wide Association Study, GWAS）结果进行了整合。基因组预测结果显示，在不同环境间以及使用独立数据集时，两个性状均表现出正向预测能力（0.34-0.50），但在马里兰州的环境中，针对种子休眠性存在显著差异的DNA混合样本，其预测能力有所下降（0.07-0.15）。通过混合DNA样本，我们共鉴定出6个错误发现率q值<0.01的与种子休眠性相关的显著数量性状位点（QTL）……

本研究的样本来自覆盖作物育种网络（Cover Crop Breeding Network）正在进行的育种评估工作。我们选取了四个环境，这些环境的种群规模充足，且在裂荚率与种子休眠性上存在显著的表型变异。在本研究后续部分，我们将采用缩写结合收获年份后两位的方式指代各试验环境：例如马里兰州贝尔茨维尔2020年与2022年的试验分别记为20MD、22MD；威斯康星州普拉里杜萨克2021年与2022年的试验分别记为21WI与22WI。20MD试验圃于2019年9月27日播种（北纬39°01′50″，西经76°55′59″，土壤类型为Russett-Christiana复合土），种植前为翻耕过的地块，撒播了草坪红羊茅（Festuca rubra L.；播种量340 kg·ha⁻¹）。2019年11月5日，对20MD试验圃喷施Raptor（咪唑喹啉酸铵盐；用量0.37 L·ha⁻¹）以防控冬季杂草。20MD试验的荚果采集时间为2020年6月23日至6月30日（采集时间因不同基因型的荚果成熟度而异，详见下文）。22MD试验圃于同一地点播种……

# 毛叶苕子混合DNA样本的SNP等位基因：聚焦裂荚率与种子休眠性相关QTL

## 数据与文件结构说明
`VetchPoolDNA_MarkerInformation.csv` 包含各单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的参考等位基因与替代等位基因信息，同时标注了对应SNP在个体测序数据中缺失数据的个体百分比，以及混合DNA测序样本中的平均测序深度。
`VetchPoolDNA_Dosage.csv` 包含等位基因剂量信息，列代表遗传位点，行代表个体或DNA混合样本（含ID列）。数据中以99表示缺失值。混合样本的等位基因频率为等位基因读取频率的平均值，因此二者的数值尺度存在差异：个体样本的取值范围为0-2，混合样本的取值范围为0-1。
`VetchPoolDNA_Performance.csv` 包含各DNA混合样本的裂荚率、种子休眠率以及纳入表型信息的个体数量。

## 共享与获取说明
本文件中的个体……