Browsing by Browse by SEO 2008 "820203 Citrus Fruit"

'Citrus' taxonomy is very complex mainly due to specific aspects of its reproductive biology. A number of studies have been performed using various molecular markers in order to evaluate the level of genetic variability in 'Citrus'. SNP markers have been used for genetic diversity assessment using a variety of different methods. Recently, the availability of EST database and whole genome sequences has made it possible to develop more markers such as SNPs. In the present study, the high-resolution melting curve analysis (HRM) was used to detect SNPs or INDELs in 'Citrus' genus for the first time. We aimed to develop a panel of SNPs to differentiate 'Citrus' genotypes which can also be applied to 'Citrus' biodiversity studies. The results showed that 21 SNP containing markers produced distinct polymorphic melting curves among the 'Citrus' spp. investigated through HRM analysis. It was proved that HRM is an efficient, cost-effective, and accurate method for discriminating citrus SNPs as well as a method to analyze more polymorphisms in a single PCR amplicon, representing a useful tool for genetic, biodiversity, and breeding studies. SNPs developed based on 'Citrus sinensis' EST database showed a good transferability within the 'Citrus' genus. Moreover, HRM analysis allowed the discrimination of citrus genotypes at specific level and the resulting genetic distance analysis clustered these genotypes into three main branches. The results suggested that the panel of SNP markers could be used in a variety of applications in citrus biodiversity assessment and breeding programs using HRM analysis.

The overall aim of this project was to identify constraints that impede smallholders' capacity to adopt innovative farming practices and better marketing strategies to improve farm-level productivity and profitability. The key objectives of this SRA were: • To understand the technological, institutional and capacity constraints that cause a wide range of differences in productivity outcomes for smallholders. • To identify the main factors influencing productivity improvement for farmers and the kind of policy measures can be adopted to improve these criteria. • To review the marketing strategies adopted by smallholders to maximize their returns and, thus, identify policy options to accelerate market reform. • To evaluate: (a) the agricultural support strategies implemented by the government and donors to increase farm productivity, and (b) the capacity of these strategies to support productivity development. This research that addressed these objectives involved several stages, including: (a) reviewing the literature and analysing the existing policies to promote pro-poor agricultural growth; (b) developing survey tools and econometric methods to measure the main sources of horticultural sector performance and various constraints that are hindering smallholders' productivity and profitability; (c) policy workshop(s) and consultation with stakeholders including academics, government officials, international donors and industry representatives; (d) focus-group interviews with smallholders to identify priority area for reform; and (e) dissemination of research findings through conference participation and policy briefs.

Citrus taxonomy is very complex mainly due to specific aspects of its reproductive biology. A number of studies have been performed using various molecular markers in order to evaluate the level of genetic variability in citrus. SNP markers were used for genetic diversity assessment using different methods; recently, the availability of EST database and whole genome sequences increased the information on sequence variability in citrus leading to wider employment of these markers so that reliable SNP detection methods are needed. In the present study, for the first time we applied high resolution melting curve analysis (HRM) in citrus to detect the presence of SNPs polymorphisms and their involvement in functional and structural genomics. In citrus, the possibility of characterizing genetic diversity was drastically increased using this method since it allowed analyzing more polymorphisms in a single PCR fragment. Furthermore, we identified SNPs associated with gene coding regions which revealed some aspects of their functionality in biochemical variations. The results suggested that HRM is an efficient, cost-effective and accurate method to detect sequence variations. In fact, HRM analysis provided a panel of primers for HRM genotyping in citrus representing also a useful tool for bridging functional and structural genomics.

High resolution melting curve analysis (HRM) has been used as an efficient, accurate and cost-effective tool to detect single nucleotide polymorphisms (SNPs) or insertions or deletions (INDELs). However, its efficiency, accuracy and applicability to discriminate microsatellite polymorphism have not been extensively assessed. The traditional protocols used for SSR genotyping include PCR amplification of the DNA fragment and the separation of the fragments on electrophoresis-based platform. However, post-PCR handling processes are laborious and costly. Furthermore, SNPs present in the sequences flanking repeat motif cannot be detected by polyacrylamide-gel-electrophoresis based methods. In the present study, we compared the discriminating power of HRM with the traditional electrophoresis-based methods and provided a panel of primers for HRM genotyping in Citrus. The results showed that sixteen SSR markers produced distinct polymorphic melting curves among the 'Citrus spp' investigated through HRM analysis. Among those, 10 showed more genotypes by HRM analysis than capillary electrophoresis owing to the presence of SNPs in the amplicons. For the SSR markers without SNPs present in the flanking region, HRM also gave distinct melting curves which detected same genotypes as were shown in capillary electrophoresis (CE) analysis. Moreover, HRM analysis allowed the discrimination of most of the 15 citrus genotypes and the resulting genetic distance analysis clustered them into three main branches. In conclusion, it has been approved that HRM is not only an efficient and cost-effective alternative of electrophoresis-based method for SSR markers, but also a method to uncover more polymorphisms contributed by SNPs present in SSRs. It was therefore suggested that the panel of SSR markers could be used in a variety of applications in the citrus biodiversity and breeding programs using HRM analysis. Furthermore, we speculate that the HRM analysis can be employed to analyse SSR markers in a wide range of applications in all other species.