Geographic Description of Genetic Diversity and Relationships in the USDA Rice World Collection

Abstract

Knowledge of genetic diversity and relationships among global germplasms of rice collected by the USDA since 1866 is critical for utilization, conservation, and management of the collection. A core subset developed from this collection, including 1794 accessions obtained from 112 countries in 14 geographic regions, was genotyped with one indel and 71 simple sequence repeat (SSR) markers. Total alleles were 1005, averaging 14 alleles per locus. A great majority of genetic variance was due to within instead of among geographic regions and within instead of among countries. The regions and countries were highly and significantly differentiated using these markers. Germplasm accessions obtained from the southern Asia, Southeast Asia, and Africa were highly diversified, while those from North America and western and eastern Europe had the lowest diversity. Different measurements of genetic diversity, including average number of alleles per locus, polymorphism information content (PIC), Nei index, and average number of private alleles per locus uniformly reached this conclusion. Three main clusters were revealed by both analyses of principal coordinates and Nei genetic similarities for the 14 regions. Seventy‐eight countries, from which five or more accessions were collected in the core subset, were differentiated into five main clusters. Germplasm accessions obtained from Myanmar, Indonesia, Cambodia, Malaysia, and Nepal were highly diversified, while those from France, Spain, Romania, Italy, and the United States were poorly diversified. This study proves that the USDA global collection effectively supports the U.S. rice industry with vast genetic diversity responsive to biotic and abiotic stresses.

Assessment of the genetic diversity and population structure in temperate japonica rice germplasm used in breeding in Chile, with SSR markers

“…Gene diversity means for the entire population, indica and japonica were 0.54, 0.48, and 0.45, respectively. Yan et al (2010) studied a USDA world rice collection of 1794 accessions from 112 countries in 14 geographic regions, which reported a major allele frequency of 0.52, mean alleles per locus of 7.8, gene diversity of 0.61, and PIC value of 0.57.…”

Worldwide Genetic Diversity for Mineral Element Concentrations in Rice Grain

“…Seed samples for grain ionomic analyses were produced in small field plots in Beaumont, TX, using the same planting, field management, and harvest methods used in companion studies (Norton et al, 2012, 2014; Zhang et al, 2014). Because availability of many elements in soil is known to be greatly affected by soil redox potential, this rice grain study evaluated grains from the same set of diverse rice accessions grown over 2 yr under both flooded (anaerobic) and unflooded (aerobic, flush irrigated) irrigation schemes.…”

Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal

“…In addition to these cultivars, 31 aus accessions from Bangladesh or India were selected from the Rice Diversity Panel 1 (Zhao et al, 2011). A total of 27 known aus accessions originating from Bangladesh or India were also obtained from the USDA core rice collection (Yan et al, 2010). A further 41 cultivars were collected by Bangladesh Agricultural University from sources in Bangladesh, including both landraces and improved cultivars.…”