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United States Department of Agriculture

Agricultural Research Service

Title: Genotypic and phenotypic assessment of the NSGC rice core collection for amylose content and alkali spreading value

item Fjellstrom, Robert
item Yan, Wengui

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 1, 2006
Publication Date: February 15, 2006
Citation: Fjellstrom, R.G., Yan, W., Chen, M.H., Bryant, R.J., Bockelman, H.E., McClung, A.M. 2006. Genotypic and phenotypic assessment of the NSGC rice core collection for amylose content and alkali spreading value. In: Proceedings of the 30th Rice Technical Working Group Meeting. 2006 CDROM.

Technical Abstract: The USDA-ARS National Small Grains Collection (NSGC) Oryza germplasm collection currently contains over 20,000 rice accessions. A core subset of roughly 1600 accessions was made in 2001 to represent the genetic spectrum of the rice germplasm collection. Core collections are being established for many species to enhance the efficiency of identifying new and useful source materials and, consequently, reduce costs in identifying desirable genes. The NSGC rice core, derived from some 100 countries, was grown in Stuttgart, AR during 2002 for phenotypic and genotypic evaluation. Cooking quality is one of the most important traits in rice, with the two foremost components being amylose content and gelatinization temperature. Detailed biochemical and genetic studies have shown that the rice Waxy gene, which encodes the granule bound starch synthase enzyme, controls grain amylose content. Comprehensive studies have also shown that the Alk gene, which encodes the soluble starch synthase IIa enzyme, controls starch gelatinization temperature (frequently measured as alkali spreading value, or ASV) by regulating starch amylopectin chain lengths. In this research, over 1600 accessions of the USDA rice core collection were phenotyped for amylose content and ASV. These accessions were also genotyped for two SNP (i.e., single nucleotide polymorphism) markers associated with amylose content (exon 1 and exon 6), one SNP marker associated with starch pasting (RVA) properties (exon 10), and an intragenic microsatellite (RM 190), all in the rice Waxy gene, as well as two SNP markers in the Alk gene associated with ASV. Fourteen alleles for the Waxy microsatellite marker were identified, six of which were rare, each being found in less than 1% of the accessions. Accessions with 8, 10, 11, or 12 CT repeats in the Waxy microsatellite marker all had high (>22%) amylose content, while each of the few accessions with 14, 21, or 22 CT repeats had intermediate (20-22%) amylose content. Accessions having 13, 15, 16, 17, 18, 19, and 20 CT repeats had either low (4-19%), intermediate, or high amylose content, such that these microsatellite alleles were not highly correlated with any one amylose content level. We found that the SNPs at exon 1 or 6 of the Waxy gene were better indicators of amylose content than microsatellite alleles. Jodon, L-202, and Cocodrie are examples of cultivars having the same Waxy microsatellite allele as cultivars like Cypress, Lemont, and Jefferson but they have significantly higher amylose content. Our results indicate that allelic variation at exon 6 in these cultivars results in increased amylose content, but reduced RVA paste viscosity. Although amylose content explains some of the variation in starch pasting properties, a SNP in exon 10 of the Waxy gene appears to significantly affect RVA measurements independent of amylose content. One allele of this SNP is associated with a distinct RVA curve that is indicative of superior processing and parboiling quality. These results demonstrate that although the RM190 marker, which is a microsatellite in the non-coding region of the Waxy gene, is useful for predicting cooking quality in a narrow germplasm base, allelic variation in other coding regions of Waxy have been identified that offer greater accuracy in prediction of rice cooking and processing quality. We have also seen that there is no single SNP or mutation shared among ‘waxy’ (glutinous) rice accessions that have no measurable amylose. Other researchers have demonstrated that a wide variety of mutations in the Waxy gene can abolish granule bound starch synthase enzyme activity, resulting in no amylose being produced. Over 60% of the accessions had the same alleles at the two Alk gene SNP sites which were associated with intermediate or high ASV. However, mutations shown at either of the two SNPs resulted in ASV readings indicating low gelatinization temperatures in the core accessions. Thirty percent of the accessions possessed a SNP mutation commonly found in medium and small grain USA germplasm and 9% of the accessions had a SNP mutation found primarily in northeast Asian germplasm. A small number of accessions had low gelatinization temperatures with neither SNP mutation, suggesting the presence of other genes affecting amylopectin properties besides the specific Alk gene SNPs assayed. Our results demonstrate that molecular marker evaluation provides a valuable method for characterizing world germplasm that is not skewed by environmental error, reveals sample heterogeneity that may be obscured in phenotypic evaluation, and clearly identifies novel alleles within a continuous spectrum of phenotypes.

Last Modified: 9/10/2014
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