ABSTRACT

Groundnut (Arachis hypogaea L.) is an important crop internationally for both direct human consumption and as an oilseed crop, which is being cultivated in 108 countries of the world. About two thirds of world groundnut production comes from the semi-arid tropic (SAT) regions which are characterized by uncertain rainfall and frequent droughts. Groundnut yields are low and average about 0.8 t/ha in the SAT countries compared to more than 2.6 t/ha of the developed world.

One contribution to increasing yield is development of early maturing, high yielding cultivars that are needed for short growing seasons, multiple cropping systems, and which avoid late season droughts. In most breeding programs few sources of early maturity have been used resulting in the narrow genetic base of groundnut cultivars. There is a need for broadening the genetic base to enhance groundnut breeding prospects. The high diversity detected by SSR markers is consistent with the known characteristics – that they are more variable and high expected heterozygosity than the RAPDs, or AFLPs. The high levels of polymorphism associated with SSRs are expected because of unique evolution of these genomic regions: replication slippage rather than mutations, insertions or deletions.

The present study was initiated to assess diversity using SSR markers among 29 groundnut accessions belonging to two subspecies fastigiata and hypogaea and three botanical varieties vulgaris, fastigiata, and hypogaea, originating from fifteen countries which include 25 early-maturing and 4 late-maturing accessions. Initially 7 to 10 individual plants from each of ten accessions were assayed for intra-accession variation using 5 SSR primer pairs. These ten accessions include ICG 3540, ICG 4558, ICG 4890, ICG 9427, ICG 11914, ICG 14814, Gangapuri, JL 24, Chico, and TMV2. UPGMA clustering of the SSR band profiles revealed significant variation within the accessions. A total of 22 alleles were detected by five primer pairs with an average number of 4.4 alleles per primer pair. The number of alleles ranged from 2 alleles for 2B10 to 8 alleles for 2D12B. To capture this intra-accession diversity in the main study equal amounts of DNA from individual plants were pooled for each accession.

Inter-accession diversity analysis of 29 accessions was performed using 20 SSR primer pairs, which detected a total of 57 alleles with an average of 2.85 alleles per primer pair. The number of alleles per marker ranged from two to five. The PIC values, ranged from 0.53 (17F6) to 0.93 (15C12), with an average of 0.78. The AMOVA analysis indicated 42% of variation in SSR markers used between early and late-maturing accessions.  The clustering revealed significant diversity among the 29 accessions used for this study. The different botanical varieties were grouped into 3 different clusters except one accession. The MDS analysis supported the clustering obtained by UPGMA. Clustering also revealed significant diversity among accessions within a particular country. Comparison of genotypic data with phenotypic data for these accessions may project the complete picture of diversity. This analysis will assist groundnut breeding programs aimed at improving early-maturity to maximize the genetic base of their breeding populations.