Genotyping accessions in the National Small Grains rice collection to enable curation and identification of accessions with traits useful for U.S. rice breeders

Authors: Huggins, Trevis; Edwards, Jeremy; McClung, Anna; Jia, Melissa

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/11/2023
Publication Date: 1/30/2024
Citation: Huggins, T.D., Edwards, J., McClung, A.M., Jia, M.H. 2024. Genotyping accessions in the National Small Grains rice collection to enable curation and identification of accessions with traits useful for U.S. rice breeders [abstract]. Proceedings of 39th Rice Technical Working Group meeting, Hot Springs, Arkansas, February 20-23, 2023. p. 62.

Interpretive Summary:

Technical Abstract: Germplasm collections house and safeguard the genetic diversity of the world’s food crops and related wild species. Plant breeders can use this valuable genetic diversity to improve agricultural productivity, disease resistance, and nutritional quality. However, the majority of germplasm collections only possess phenotypic characterization data. The addition of genetic marker data to the germplasm collection can add greater value for use in breeding programs. The National Small Grains Collection (NSGC) contains about 19,000 rice accessions, of which about 3,450 have been genotyped with 11 fingerprint markers (FPM), 14 trait specific markers (TSM), and one subspecies marker. The genetic markers identify the presence of alleles affecting traits such as plant height, apparent amylose content, starch pasting properties, gelatinization temperature, blast resistance, bran color, aroma, and pubescence, as well as classify accessions by species (e.g., O. sativa or O. glaberrima), and sub-species within O. sativa as indica or japonica. The genotyping of 3,450 accessions revealed that most have one or more blast resistance alleles, a small number have the semi-dwarf allele, and almost all are pubescent. About 41% of the accessions were identified as high amylose types, while 19 % were intermediate and 23% were low amylose types. Most of the accessions possess the allele for intermediate gel temperature and a moderate number possess the allele for low gel temperature. The number of high gel temperature accessions are very low. This is because accessions with high gel temperature occurs when accessions with the intermediate gel temperature allele also have low amylose. The addition of genotypic data to the GRIN-Global database will benefit U.S. rice breeders by providing them with genetic information, allowing them to select accessions with novel and useful alleles that are not available within their breeding lines. Accessions classified as O. glaberrima in the NSGC world rice collection was previously based on their documented country of origin. This best guess approach resulted in misclassification of O. sativa as O. glaberrima and vice versa. This was also the case for accessions classified as subspecies indica or japonica. The development of the species and subspecies markers will eliminate this best guess approach and correctly classify each accession. This will allow breeders to have the relevant information needed to broaden their genetic base when selecting parents. The combination of the new genetic data, along with the phenotypic and origin data will allow breeders to more wisely select germplasm that is likely to have a direct impact and will better fit into their breeding objectives.