Mapping quantitative trait loci for important agronomic traits in finger millet (Eleusine coracana) mini core collection with genomic and genic SSR markers
- 42 Downloads
Allele identification for agro-morphological traits and stress resistance is a major concern across the globe for improving productivity of finger millet. Here, we used 46 genomic and 58 genic simple sequence repeats (SSRs) markers in a set of 66 accessions used to constitute a global mini-core collection for analysing their genetic structure as a population and establishing association among markers and twenty morphological traits including resistance to finger blast. Phenotypic data revealed a wide range of variation for all traits except flag leaf width and flag leaf sheath width. We got amplification of 81 alleles by the 31 genomic SSRs at an average of 2.61 alleles per locus. Polymorphism information content (PIC) values varied from 0.21 to 0.75 and average gene diversity was 0.49. Structure analysis of the population using the genomic SSR data divided the accessions into two clusters where Indian and exotic accessions were grouped in separate clusters. Genic SSRs which were associated with blast resistance genes, amplified 36 alleles at an average of 2 alleles per locus. PIC values ranged from 0.32 to 0.37 and average gene diversity was 0.45. Population structure analysis using data from these SSRs grouped the accessions into three clusters, which broadly correspond to their reaction to blast disease. Twenty-two significant associations were found using the GLM approach for 20 agro-morphological traits both in 2012 and 2014, while, 7 and 5 significant marker-trait associations were identified using MLM in 2012 and 2014 respectively. The SSR markers FMBLEST35 and FMBLEST36 designed from the Pi21 gene sequence of rice were found to be associated with blast disease resistance in finger millet indicating that the gene homologues play a significant role in an important role for neck blast resistance.
KeywordsFinger millet Association mapping Population structure SSR Blast
The work was supported by the Institute grant received from Indian Council of Agricultural Research, New Delhi, India. Authors are thankful to Mr. G.S. Bisht, technical officer, ICAR-VPKAS, Almora for assistance in phenotypic data generation.
The Study was funded by Indian Council of Agricultural Research.
Compliance with ethical standards
Conflict of interest
Authors declare that they have no conflict of interest.
- Bharathi A (2011) Phenotypic and genotypic diversity of global finger millet (Eleusine coracana (L.) Gaertn.) composite collection. Dissertation, Tamil Nadu Agriculture University, IndiaGoogle Scholar
- IBPGR (1985) Descriptors for finger millet. International Board for Plant Genetic Resources Secretariat, Rome, Italy. http://www.bioversityinternational.org. http://www.bioversityinternational.org/fileadmin/user_upload/online_library/publications/pdfs/417.pdf. Accessed 2 Feb 2017
- Nagaraja A, Jagadish PS, Ashok EG, Krishne Gowda KT (2007) Avoidance of finger millet blast by ideal sowing time and assessment of varietal performance under rainfed production situations in Karnataka. J Mycopathol Res 45(2):237–240Google Scholar
- Pritchard JK, Wen W (2003) Documentation for the structure software, version 2. Department of Human Genetics, University of Chicago, Chicago. http://pritchardlab.stanford.edu/software/readme_2_1/. Accessed 2 Feb 2017
- Ramakrishnan M, Antony Ceasar S, Duraipandiyan V, AlDhabi NA, Ignacimuthu S (2016a) Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers. SpringerPlus 5:120CrossRefGoogle Scholar
- Ramakrishnan M, Antony Ceasar S, Duraipandiyan V, AlDhabi NA, Ignacimuthu S (2016b) Using molecular markers to assess the genetic diversity and population structure of finger millet (Eleusine coracana (L.) Gaertn.) from various geographical regions. Genet Resour Crop Evol 63(2):361–376CrossRefGoogle Scholar
- Rao ANS (1990) Estimates of losses in finger millet (Eleusine coracana) due to blast disease (Pyricularia grisea). J Agric Sci 24:57–60Google Scholar
- Roy S, Banerjee A, Mawkhlieng B, Misra AK, Pattanayak A, Harish GD, Singh SK, Ngachan SV, Bansal KC (2015) Genetic diversity and population structure in aromatic and quality rice (Oryza sativa L.) landraces from north-eastern India. PLoS ONE 10(6):e0129607. https://doi.org/10.1371/journal.pone.0129607 CrossRefPubMedPubMedCentralGoogle Scholar