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New microsatellite markers for pigeonpea (cajanus cajan (L.) millsp.)

DOI: 10.1186/1756-0500-2-35

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Abstract:

Primers were designed for 113 pigeonpea genomic SSRs, 73 of which amplified interpretable bands. Thirty-five of the primers revealed polymorphism among 24 pigeonpea breeding lines. The number of alleles detected ranged from 2 to 6 with a total of 110 alleles and an average of 3.1 alleles per locus. GT/CA and GAA class of repeats were the most abundant di-nucleotide and tri-nucleotide repeats respectively. Additionally, 220 soybean primers were tested in pigeonpea, 39 of which amplified interpretable bands.Despite the observed morphological diversity, there is little genetic diversity within cultivated pigeonpea as revealed by the developed microsatellites. Although some of the tested soybean microsatellites may be transferable to pigeonpea, lack of useful polymorphism may hinder their full use. A robust set of markers will still have to be developed for pigeonpea genome if molecular breeding is to be achieved.The increasing concern of the effect of global climate change and its likely impact on agriculture has stimulated scientists to search for crops that can withstand extreme environmental conditions. Among legumes, pigeonpea {Cajanus cajan (L.) Millspaugh} (2n = 22) has attracted attention as being both drought-tolerant [1] and highly nutritious [2]. Extensive morphological variation within the genus Cajanus as a whole and in cultivated species in particular has always led to the assumption that there exists abundant genetic diversity within the cultivated species. To the contrary, molecular studies have reported extremely low levels of polymorphism within the cultivated species compared to its wild relatives [3,4]. Such findings suggest that efforts towards the development of a linkage map of pigeonpea should focus on the use of an interspecific cross, and the development of a substantially high number of markers. We report the development of new 36 polymorphic simple sequence repeat (SSR) markers that will be an asset in characterising and understanding the nat

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