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CROP BREEDING, GENETICS & CYTOLOGY

A Marker-Based Approach to Broadening the Genetic Base of Rice in the USA

^a Dep. of Plant Breeding, Cornell Univ., Ithaca, NY 14853-1901
^b RiceTec, Inc., P.O. Box 1305, Alvin, TX 77512

^* Corresponding author (SRM4{at}cornell.edu)

The narrow genetic base of U.S. rice (Oryza sativa L.) cultivars poses a challenge for long-term improvements of yield and other agronomic traits. Molecular marker analysis can be used to quantify the diversity of U.S. rice varieties in comparison with worldwide germplasm accessions and can provide useful information for developing rational strategies to broaden the genetic base of U.S. rice. In this study, the genetic diversity of 236 rice accessions was investigated on the basis of genotypic evaluation at 113 restriction fragment length polymorphism (RFLP) and 60 simple sequence repeat (SSR) loci. A total of 274 RFLP and 714 SSR alleles were detected in the entire dataset. The average polymorphism information content (PIC) values were 0.36 for the RFLP and 0.66 for the SSR markers. The entire 236-accession collection was analyzed as two subsets: the U.S. collection, consisting of 125 cultivars bred in the USA, and the world collection, consisting of 111 diverse rice accessions collected from 22 other countries around the world. The accessions from the world collection represented 99% of the total RFLP and 96% of the SSR diversity, while the cultivars from the USA contained 82% of RFLP and 56% of SSR alleles. Significant differences in allele frequencies were observed between the world and U.S. collections and between older U.S. cultivars and their modern derivatives. A diverse subset of 31 rice cultivars (13% of the 236 cultivars) was identified that embodied 95% of RFLP and 74% of SSR alleles. This subset can be used in the development of core collections and offers an efficient source of genetic diversity for future crop improvement.

Abbreviations: PIC, polymorphism information content • RFLP, restriction fragment length polymorphism • RS, random selection • SAF, shared allele frequency • SSR, simple sequence repeat

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