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Lodi Vecchio, Italy

Stevanato P.,University of Padua | Biscarini F.,FPTP
Sugar Tech | Year: 2015

Real-time PCR (qPCR) allelic discrimination and high-resolution melting (HRM) methods are widely adopted for the detection of single nucleotide polymorphisms (SNP). Digital PCR (dPCR) is a new method recently proposed for the detection of low-frequency and/or rare SNP. The molecular marker SNP_BvBTC1 is used in sugar beet to distinguish between annual and biennial flowering plants. The CC genotype at this SNP locus is associated with biennial beets, while the CA and AA genotypes are typically found in annual beets. In this study, we compared the sensitivity of qPCR, HRM and dPCR in detecting the allele A from two pools of bulk beet DNA composed of 90 biennial + 10 annual plants (B1) and 99 biennial + 1 annual plant (B2), respectively. All annual plants were found to have the AA genotype. qPCR could not detect allele A in either the B1 or B2 pool and HRM detected allele A only at moderate frequencies (10 %), in the B1 pool. dPCR, on the contrary, was able to detect allele A in both pools. We therefore concluded that dPCR is a suitable method for the quantitation of SNP_BvBTC1 within bulked DNA samples of sugar beet. © 2015 Society for Sugar Research & Promotion Source


Ahmadi N.,CIRAD - Agricultural Research for Development | Negrao S.,New University of Lisbon | Negrao S.,Institute Biologia Experimental e Tecnologica | Katsantonis D.,Greek National Agricultural Research Foundation | And 13 more authors.
Theoretical and Applied Genetics | Year: 2011

During the last decade, a large number of QTLs and candidate genes for rice tolerance to salinity have been reported. Using 124 SNP and 52 SSR markers, we targeted 14 QTLs and 65 candidate genes for association mapping within the European Rice Core collection (ERCC) comprising 180 japonica accessions. Significant differences in phenotypic response to salinity were observed. Nineteen distinct loci significantly associated with one or more phenotypic response traits were detected. Linkage disequilibrium between these loci was extremely low, indicating a random distribution of favourable alleles in the ERCC. Analysis of the function of these loci indicated that all major tolerance mechanisms were present in the ERCC although the useful level of expression of the different mechanisms was scattered among different accessions. Under moderate salinity stress some accessions achieved the same level of control of Na + concentration and Na +/K + equilibrium as the indica reference variety for salinity tolerance Nona Bokra, although without sharing the same alleles at several loci associated with Na + concentration. This suggests (a) differences between indica and japonica subspecies in the effect of QTLs and genes involved in salinity tolerance and (b) further potential for the improvement of tolerance to salinity above the tolerance level of Nona Bokra, provided the underlying mechanisms are complementary at the whole plant level. No accession carried all favourable alleles, or showed the best phenotypic responses for all traits measured. At least nine accessions were needed to assemble the favourable alleles and all the best phenotypic responses. An effective strategy for the accumulation of the favourable alleles would be marker-assisted population improvement. © 2011 Springer-Verlag. Source


Broccanello C.,University of Padua | Stevanato P.,University of Padua | Biscarini F.,FPTP | Cantu D.,University of California at Davis | Saccomani M.,University of Padua
BMC Genetics | Year: 2015

Background: Premature flowering or bolting is an undesirable characteristic that causes severe sugar yield losses and interferes with harvesting. Vernalization is a prerequisite for the floral induction, achieved by exposure to low temperatures for 10-14 weeks. This process is also controlled by other environmental factors, such as long daylight photoperiods and a combination of genetic factors. The objective of this study was the identification of new genetic polymorphisms linked to bolting tendency in sugar beet. Results: Two pollinators characterized by low and high bolting tendency were subjected to RAD-sequencing in order to detect discriminating SNPs between lines. 6,324 putative SNPs were identified. Of these, 192 were genotyped in a set of 19 pollinators, each comprising bolted and non-bolted individuals, for a total of 987 samples. Among the 192 candidate SNPs, the strongest overall association was found for SNP183 on chromosome 6 (p-value = 1.246·10-13). The association between SNP183 and bolting tendency was then confirmed in an independent population of 730 plants from 11 breeding lines (p-value = 0.0061). SNP183 is located in the intron of Bv_22330_orky, a sugar beet homolog of a matrix metalloproteinase (MMP) gene that could be implied in flowering in Arabidopsis thaliana. Conclusion: Our data support a significant association between an intronic SNP in the MMP gene located on chromosome 6 and the regulation of bolting tendency in sugar beet. The newly identified locus supports the polygenic nature of flowering control. The associated marker can be used to design SNP panels for the discrimination of bolters and non-bolters, to be used in sugar beet breeding programs for the development of improved germplasm with low bolting tendency. © 2015 Broccanello et al. Source

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