Enhancing the searchability, breeding utility, and efficient management of germplasm accessions in the USDA−ARS rice collection

Abstract

Genebanks conserve worldwide crop genetic diversity in systematically assembled and maintained ex situ collections for use by plant breeders and geneticists to improve the productivity, value, and sustainability of agriculture. Challenges faced in genebank management include providing sufficient and accurate trait information to facilitate searching the collection; controlling redundant accessions, seed mixtures, and mislabeled accessions; and identifying gaps in diversity. To help address these issues, a system that employs genotyping using 24 trait‐specific markers (TSMs), fingerprint markers (FPMs), or markers that are unique to subspecies was implemented for the USDA–ARS National Plant Germplasm System (NPGS), National Small Grains Collection (NSGC) for rice (Oryza sativa L.). Trait‐specific markers were used to validate phenotypic data for fragrance, pericarp color, apparent amylose content, starch pasting properties, gelatinization temperature, resistance to rice blast disease, plant pubescence, and plant height. Discrepancies between genotypic and phenotypic data are useful for quality control during curation or may present opportunities for identifying novel alleles, particularly for TSMs. Over 2,000 accessions were classified by species, O. sativa or O. glaberrima Steud.; subspecies, Indica or Japonica; and subpopulation, aromatic, indica, aus, temperate japonica, or tropical japonica using the subspecies marker and FPMs. This small panel of TSMs and FPMs was also adequate for differentiating important U.S. cultivars, which are primarily of tropical japonica background. As a result of this study, TSM and FPM descriptors will be added to the rice NSGC database, redundancies reduced, and mislabeled accessions corrected, thus increasing the value of the rice NSGC for breeding programs and providing new opportunities for gene discovery.

Grain Size Selection Using Novel Functional Markers Targeting 14 Genes in Rice

“…We concluded four FNPs might contribute to the grain size difference between the two japonica subpopulations, namely, qLGY3_SNP, GW5_InDel, GLW7_InDel and GL7_InDel1, because the allele ratio is differentiated between the subpopulations (96%, 76%, 86% and 84% for allele 1 in Tej and 90%, 83%, 89% and 94% for allele 2 in Trj for four FNPs, respectively). This allele distribution might explain why Tej accessions have wider but shorter grains in contrast to Trj accessions as shown in previous studies (Ali et al 2011;McClung et al 2020;Zhao et al 2011).…”

“…In the future, it will be important to clarify the novel loci for these subspecies differences in segregating populations. Although there is a known close relationship between the aus and indica subpopulations composing the indica subspecies and similarly between temperate japonica (Tej) and tropical japonica (Trj) subpopulations composing the japonica subspecies, significant difference in grain size were noted between the Tej and Trj subpopulations, suggesting grain size is an important driver of subpopulation structure (Ali et al 2011;McClung et al 2020;Zhao et al 2011). To investigate this relationship, we used our data to compare the grain size traits of four subpopulations (Table S2 and Table S3), and found significant differences between the Tej and Trj subpopulations for all four grain size traits but no difference between the aus and indica subpopulations, consistent with the previous results from different locations.…”

Registration of twoOryza sativatropicaljaponicagermplasm lines selected for panicle architecture and grain size traits

“…The commercial check cultivars developed for production in the southern United States included ‘Mermentau’ (PI 665688), a long‐grain cultivar having 22.6% apparent amylose content and an alkali spreading value of 4.0 indicating an intermediate gelatinization temperature, which was released in 2012 (Oard et al., 2014), and ‘Titan’ (PI 680613), a medium‐grain cultivar having 15.0% apparent amylose content and an alkali spreading value of 7.0 indicating a low gelatinization temperature, which was released in 2017 (Sha et al., 2018). More recently, the aforementioned markers for grain quality (RM190, Wx In1 and Wx Ex6, and Alk ) confirmed that Mermentau had an intermediate amylose content and intermediate gelatinization temperature and Titan had a low amylose content and low gelatinization temperature (McClung et al., 2020). The study was conducted in a randomized complete block design with four replications.…”

“…Estrela (GSOR 301227) is a cultivar originating from Colombia that is an extra‐long grain with low amylose content and high gelatinization temperature based on marker alleles for RM190, Wx In1 and Wx Ex6, and Alk (Eizenga et al., 2014; McClung et al., 2020), it possesses the Pi‐z (Fjellstrom et al., 2006) and Pi‐ks (Fjellstrom et al., 2004) major genes for resistance to rice blast disease, and is pubescent. The NSFTV199 parent (GSOR 301190) is of unknown origin and is a medium grain with intermediate amylose content and intermediate gelatinization temperature based on marker alleles for these genes (Eizenga et al., 2014; McClung et al., 2020). The plant is glabrous, and it possesses the Pi‐ks rice blast resistance gene (Eizenga et al., 2014; Eizenga, Jia, et al., 2019).…”

Evaluation of Guangxi common wild rice for resistance to brown planthopper using a new stem evaluation method

“…Molecular markers play an important role in the identification and characterization of new germplasm (O'Neill et al., 2003), and simple sequence repeat (SSR) markers are often used to analyze the genetic diversity of rice. The ability of SSR markers to differentiate rice accessions genotypically is documented by the fact that a “fingerprint marker” panel consisting of 12 SSR markers differentiated a diverse subset of nearly 2,000 O. sativa accessions from the U.S. germplasm collection, and with two additional SSR markers, the identity of nearly 95 U.S. varieties that are closely related was ascertained (McClung et al., 2020). The rich genetic diversity found in common wild rice ( O. rufipogon ) accessions from Southeast Asia, mainly China, has been documented in several studies involving 90–4,173 accessions genotyped with 24–46 SSR markers (Li et al., 2010; Pan et al., 2018; Sun & Yang, 2009; Xue et al., 2016), confirming the ability of SSR markers to document the genetic diversity in this ancestral wild species.…”