title: Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis.
abstract: Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.
authors.affiliation: Biotechnology Division, UP Council of Sugarcane Research, Shahjahanpur 242001, India; Interdisciplinary Programme of Life Science for Advance Research and Education, University of Rajasthan, Jaipur 302004, India; Department of Botany, University of Rajasthan, Jaipur 302015, India.
authors.forename: Shamshad
authors.initials: S
authors.lastname: Ul Haq
authors.affiliation: Biotechnology Division, UP Council of Sugarcane Research, Shahjahanpur 242001, India; School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Kumar
authors.affiliation: Biotechnology Division, UP Council of Sugarcane Research, Shahjahanpur 242001, India.
authors.forename: R K
authors.initials: RK
authors.lastname: Singh
authors.affiliation: Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 302006, India.
authors.forename: Kumar Sambhav
authors.initials: KS
authors.lastname: Verma
authors.affiliation: Interdisciplinary Programme of Life Science for Advance Research and Education, University of Rajasthan, Jaipur 302004, India; Department of Botany, University of Rajasthan, Jaipur 302015, India.
authors.forename: Ritika
authors.initials: R
authors.lastname: Bhatt
authors.affiliation: Department of Botany, University of Rajasthan, Jaipur 302015, India.
authors.forename: Meenakshi
authors.initials: M
authors.lastname: Sharma
authors.affiliation: Department of Botany, University of Rajasthan, Jaipur 302015, India.
authors.forename: Sumita
authors.initials: S
authors.lastname: Kachhwaha
authors.affiliation: Interdisciplinary Programme of Life Science for Advance Research and Education, University of Rajasthan, Jaipur 302004, India; Department of Botany, University of Rajasthan, Jaipur 302015, India; Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 302006, India.
authors.forename: S L
authors.initials: SL
authors.lastname: Kothari