Multi-environment evaluation and genomic prediction of agronomic traits in the southern US rice genepool

The southern US is responsible for 80% of the country’s production of rice, approximately half of which is exported to other countries. Understanding genotypic and environmental factors impacting the historical performance of rice (Oryza sativa L.) is important for directing research efforts to optimize production of this globally important crop. A set of 429 rice genotypes including globally diverse historical parents and advanced japonica breeding lines from southern US breeding programs were phenotyped in 2008 for 8 agronomic traits in Arkansas, Louisiana, and Mississippi. These were also genotyped using a single-nucleotide polymorphism set optimized for genomic prediction/selection. Genotypic and phenotypic data were analyzed via clustering techniques, principal component analysis, and Finlay-Wilkinson regression. Single trait Genomic Best Linear Unbiased Prediction, multi-trait genomic prediction (via mega-scale linear mixed models; MegaLMM), and crop growth modeling (CERE..., , # Multi-environment evaluation and genomic prediction of agronomic traits in the southern US rice genepool

Dataset DOI: [10.5061/dryad.j9kd51ctd](https://doi.org/10.5061/dryad.j9kd51ctd)

## Description of the data and file structure

This dataset includes rice SNP data in HapMap format and phenotypic measurements of the rice in the field.

For genotyping, this rice panel was grown in a greenhouse in Stuttgart, Arkansas. Leaf disks were collected and sent to Agriplex Genomics for genotyping using the Agriplex 550 SNP Rice panel designed for GS using southern US rice germplasm (Cerioli et al., 2022). We acknowledge and thank the team at Louisiana State University that facilitated genotyping: Brijesh Angira, Tommaso Cerioli, Chris Hernandez, and Adam Famoso. Additionally, we thank Melissa Jia (Dale Bumpers National Rice Research Center) for obtaining leaf samples and preparing them for genotyping.

For phenotyping, the rice was grown in the field in three locations in 2008: at the Delta..., ,