Determination of genetic variability of traditional varieties of Brazilian rice using microsatellite markers

Abstract

The rice (Oryza sativa) breeding program of the Rice and Bean research center of the Brazilian agricultural company Empresa Brasileira de Pesquisa Agropecuária (Embrapa) is well established and provides new cultivars every year to attend the demand for improved high yielding varieties with tolerance to biotic and abiotic stresses. However, the elite genitors used to compose new populations for selection are closely related, contributing to the yield plateau reached in the last 20 years. To overcome this limit, it is necessary to broaden the genetic basis of the cultivars using diverse germplasm such as wild relatives or traditional varieties, with the latter being more practical because they are more easily crossed with elite germplasm to accelerate the recovery of modern plant types in the breeding lines. The objective of our study was to characterize the allelic diversity of 192 traditional varieties of Brazilian rice using 12 simple sequence repeat (SSR or microsatellite) markers. The germplasm was divided into 39 groups by common name similarity. A total of 176 alleles were detected, 30 of which (from 23 accessions) were exclusive. The number of alleles per marker ranged from 6 to 22, with an average of 14.6 alleles per locus. We identified 16 accessions as a mixture of pure lines or heterozygous plants. Dendrogram analysis identified six clusters of identical accessions with different common names and just one cluster with identical accessions with the same common name, indicating that SSR markers are fundamental to determining the genetic relationship between landraces. A subset of 24 landraces, representatives of the 13 similarity groups plus the 11 accessions not grouped, was the most variable set of genotypes analyzed. These accessions can be used as genitors to increase the genetic variability available to rice breeding programs.

Genetic diversity, identification, and certification of Chilean rice varieties using molecular markers

“…No identical genotypes were found within the 16 varieties (Figure 2, Table 4). A similar general mean genetic distance (0.77) was obtained in 192 traditional rice varieties from Brazil (Brondani et al, 2006). But, if only Chilean varieties are analyzed, a mean genetic distance of 0.64 was observed.…”

“…All 54 primers showed polymorphism between the 16 rice varieties and a large number of loci (30) detected 2 or 3 alleles per locus (Table 3). A higher number of alleles, with an average of 14.7 alleles per locus, were found in Brazilian varieties (Brondani et al, 2006).…”

“…This is unlike other studies where few sets of SSRs primers were used to discriminate a set hybrid (He et al, 2012) and varieties (Brondani et al, 2006;Rahman et al, 2010). On the other hand, the DNA profiles obtained with the 54 SSRs will be considered as a genetic fingerprint of the commercial rice varieties to complement agromorphological information.…”

“…Results showed a mean PIC of 0.5, which indicates that the materials evaluated were quite similar. Another rice study showed a higher PIC value (0.86) with 7 SSRs on Indian rice varieties (Rahman et al, 2010) and 0.73 using 12 SSR on 192 Brazilian rice varieties (Brondani et al, 2006). It is known that genetic material from breeding programs is more uniform because of high selection pressure and selection method.…”

Profiling of selected indigenous rice (Oryza sativa L.) landraces of Rarh Bengal in relation to osmotic stress tolerance

“…Indigenous and wild rice landraces harbour a number of favourable genes that are not expressed in the phenotype of their parents (Tanksley and McCouch 1997;Moncada et al 2001;Brondani et al 2006;Septiningsih et al 2003; Thomson et al 2007) and have been used as donor parent for different stress tolerance in a number of hybridization programmes. Osmotic stresses including drought and salinity with other adverse conditions are frequently encountered as constraint to rice production in most of the rice growing regions of Rarh Bengal (the lateritic south western districts of West Bengal).…”