Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.)

Kalyana Babu, B and Sood, S and Kumar, D and Joshi, A and Pattanayak, A and Kant, L and Upadhyaya, H D (2018) Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.). 3 Biotech (TSI), 8 (2). pp. 1-10. ISSN 2190-572X

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Abstract

Barnyard millet (Echinochloa spp.) is an important crop from nutritional point of view, nevertheless, the genetic information is very scarce. In the present investigation, rice and finger millet genomic SSRs were used for assessing cross transferability, identification of polymorphic markers, syntenic regions, genetic diversity and population structure analysis of barnyard millet genotypes. We observed 100% cross transferability for finger millet SSRs, of which 91% were polymorphic, while 71% of rice markers were cross transferable with 48% polymorphic out of them. Twenty-nine and sixteen highly polymorphic finger millet and rice SSRs yielded a mean of 4.3 and 3.38 alleles per locus in barnyard millet genotypes, respectively. The PIC values varied from 0.27 to 0.73 at an average of 0.54 for finger millet SSRs, whereas it was from 0.15 to 0.67 at an average of 0.44 for rice SSRs. High synteny was observed for markers related to panicle length, yield-related traits, spikelet fertility, plant height, root traits, leaf senescence, blast and brown plant hopper resistance. Although the rice SSRs located on chromosome 10 followed by chromosome 6 and 11 were found to be more transferable to barnyard millet, the finger millet SSRs were more polymorphic and transferable to barnyard millet genotypes. These SSR data of finger millet and rice individually as well as combined together grouped the 11 barnyard millet genotypes into 2 major clusters. The results of population structure analysis were similar to cluster analysis.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: UNSPECIFIED
Uncontrolled Keywords: Cross-genera transferability, Barnyard millet, SSR markers, Population structure, Orthologs, rice, finger millet, genomic SSRs
Subjects: Mandate crops > Millets
Mandate crops > Millets > Finger Millet
Others > Rice
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 27 Mar 2018 03:17
Last Modified: 27 Mar 2018 03:17
URI: http://oar.icrisat.org/id/eprint/10498
Official URL: http://dx.doi.org/10.1007/s13205-018-1118-1
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: The authors thank Indian Council of Agricultural Research for financial support.
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