Characterizing the genetic diversity of finger millet in Uganda

Finger millet [Eleusine corocana (L) Gaertn.] is a staple cereal, widely cultivated in the eastern, northern, northwestern, and southwestern parts of Uganda and in many other semi-arid regions of Eastern and Southern Africa as well as South Asia. The production of finger millet in Uganda is constrained by biotic and abiotic stresses, impeding the realization of yield potential. Moreover, a comprehensive review of the published literature shows that finger millet has received little research attention with limited studies conducted on diversity among Ugandan germplasm hence remaining uncharacterized, and under-utilized for breeding purposes. The objectives of this study were to (1) characterise the phenotypic diversity among the selected finger millet accessions using agronomic traits; (2) investigate the presence of pre-and post flowering drought tolerance in selected finger millet accessions; (3) determine genetic diversity among the sampled finger millet using simple sequence repeats (SSR) molecular markers; (4) determine the cross compatibility of cultivated finger millet Eleusine Corocana L with its wild relatives E. africana and E. Kigezienesis. The studies involved field evaluations conducted at the National Semi Arid Resources Research Institute (NaSARRI) Serere, Screen house experiment at Makerere University Agricultural Research Institute (MUARIK) Kabanyolo and laboratory work conducted at ICRISAT biotechnology laboratory in Nairobi, Kenya. The evaluations were conducted during first and second season rains of 2011 with a total of 400 finger millet accessions. Planting was done by hand with seeds spread in 4 rows to ensure germination using a lattice design of 16 X 25. The screen house experiments ran from March to July of 2012 with a total of 15 genotypes selected from the results of the field evaluations.10 drought tolerant, 2 varietal checks and 3 susceptible lines. The experiment was setup using a split plot design in 45 cm x 30 cm buckets with two replications. Marker characterization involved 105 finger millet accessions classified as 51 land races, 49 exotic lines, along with 5 released varieties screened against 20 polymorphic SSR markers. The determination of the cross compatibility between finger millet and the wild relatives Eleusine gnus included 18 wild collection of E africana and E kigezenesis that were crossed with E corocana species as female parents and ran from August 2011 to July 2012 at MUARIK. Analysis of variance was used to determine the agronomic trait variations, means and diversity among the accessions; the response of genotypes to post and pre flowering drought stress whereas principal component analysis was used to access the contribution of each trait to the total variation captured. Drought tolerance was investigated by measuring chlorophyll count at 1 day, 21 days and 42 days after water stress while other agronomic traits were measured using the descriptors for finger millet. The DNA extracted from the accessions were screened against 20 polymorphic SSR markers. The SSR marker PCR products were size-separated by capillary electrophoresis on an ABI 3730xl DNA analyzer (Applied Biosystems, Inc.). The fragment sizes generated from the Gene Mapper for all the 20 markers were used in the basic statistics analysis using Power Marker version 3.25, including the polymorphic information content (PIC), allelic richness, and the occurrence of unique, rare, common, and most frequent alleles. Principal coordinate analysis was computed based on Nei’s distance matrix with 1000 bootstrapping. Meanwhile successful crosses were determined by seed formation after 3-4 weeks which was followed by morphological characterization of the F1 using parent morphology and confirmed by SSR markers. Significant variations were observed among the finger millet accessions for various agronomic traits with the ear and maturity traits having the greatest contribution to the total phenotypic variation captured which was consistent with reports of previous studies. The genotypes also responded to differential pre and post flowering drought stress with significant genotype to drought treatments interaction observed for chlorophyll content 42 day after stress application and the most drought tolerant genotypes were identified. Meanwhile unique pattern of diversity was revealed by the SSR markers with a total number of 23 loci identified 226 alleles generated by 19 (out of the 20) highly polymorphic markers; alleles generated per locus ranged from 3 to 20 with an average of 9.6 alleles per locus. The polymorphic information content (PIC) varied from 0.09 to 0.88 with an average of 0.53. 62 rare alleles (27.43%), 130 common alleles (57.52%) and 34 the most frequent alleles (15.04%) and 17 most diverse accessions were also identified. Furthermore the cross between finger millet E corocana subsp corocana (2n =4x= 36), the wild relatives E corocana subsp africana and Eleusine kigezienesis (2n = 4x = 36) all allotetrapliod was successful hence compatible which was consistent with previous studies but specific to genotypes with 50% of the F1s true fertile F1 hybrids The results show that the finger millet accessions used in this study are genetically diverse and could be used to initiate a breeding program. Moreover, the gene flow within the Eleusine genus provides an opportunity for finger millet genome enhancement and improvement since varietal yield improvement is dependent on the availability of sufficient diversity. It was therefore, concluded that the diverse parents identified in this study could be used for developing finger millet populations’ for mapping contributing traits and studying their inheritance. The already identified genetically diverse and similar accessions could also be used for developing mapping populations for QTL mapping. The new sources for drought tolerance could be used for improving finger millet accessions with farmer preferred traits but there is need to evaluate them for various agronomic traits for suitability. The gene flow within the Eleusine genus could also be exploited for improving important traits such as disease resistance, drought tolerance, tillering, earliness and yields to improve the cultivated finger millet.