Non-coding RNA (ncRNA)-based SSR markers are highly useful in molecular breeding as ncRNAs play a significant role in gene regulation. In the present study, for the first time in coconut, we have identified 597 ncRNA-derived SSR markers, including 509 long non-coding RNASSRs (lncRNASSRs) and 88 micro RNASSRs (miRNASSRs). Of these, 20 primers (10 each from lncRNA-SSR and miRNA-SSR) were selected, screened on 6 coconut accessions, and 50% produced polymorphic fragments. These 10 polymorphic primers were used for genotyping 96 palms of 16 coconut accessions, comprising eight tall and dwarf accessions each. The number of alleles ranged from 2 to 9 per SSR marker, with an average of 4.6 alleles per locus. The average heterozygosity and Shannon index were 0.5 and 1.1, respectively, suggesting that ncRNA-SSRs show high polymorphism level. Distance-based cluster analyses revealed that all the tall and dwarf accessions were differentiated and grouped in different clusters. The study demonstrates the usefulness of ncRNA-based SSR markers for assessing genetic diversity and genetic improvement in coconut.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/s10142-022-00911-2 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Genome-wide development of simple sequence repeat (SSR) markers at 2-Mb intervals in lotus (Nelumbo Adans.).
BMC Genomics
January 2025
Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, No. 3888 Chenhua Road, Songjiang District, Shanghai, 201602, China.
Background: Despite the rapid advancement of high-throughput sequencing, simple sequence repeats (SSRs) remain indispensable molecular markers for various applied and research tasks owing to their cost-effectiveness and ease of use. However, existing SSR markers cannot meet the growing demand for research on lotus (Nelumbo Adans.) given their scarcity and weak connections to the lotus genome.
View Article and Find Full Text PDFRevisiting the emerging pathosystem of rice sheath blight: deciphering the virulence, host range, and rice genotype-based resistance.
Front Plant Sci
December 2024
Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta, Egypt.
Sheath blight, caused by AG1 IA, is a challenging disease of rice worldwide. In the current study, nine isolates, within the anastomosis group AG-1 IA, were isolated, characterized based on their macroscopic and microscopic features, as well as their ability to produce cell wall degrading enzymes (CWDEs), and further molecularly identified via ITS sequencing. Although all isolates were pathogenic and produced typical sheath blight symptoms the susceptible rice cultivar, Sakha 101, AG1 IA -isolate SHBP9 was the most aggressive isolate.
View Article and Find Full Text PDFSurveys of genotypes in breeding stations and commercial rice fields in Arkansas, Louisiana, and Puerto Rico from 2017 to 2019.
Plant Dis
January 2025
USDA-ARS SEA, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States;
Major resistance (R) gene mediated resistance to rice blast fungus Magnaporthe oryzae is often overcome by the fungus due to the occurrences of new races with altered corresponding avirulence (AVR) genes. In this study, blast diseased rice tissue samples were collected from breeding stations and commercial rice fields in Arkansas, Louisiana, and Puerto Rico during 2017-2019 to determine the efficacy of major R genes, Pi-ta, Pik, Pizt, Pi9, and Pi33. A total of 185 blast isolates were isolated from the diseased tissue samples to examine the existence of AVR genes AVR-Pita1, AVR-Pib, AVR-Pik, AVR-Pizt, AVR-Pi9 and ACE1.
View Article and Find Full Text PDFIdentification of blast resistant finger millet (Eleusine coracana L.) genotype through phenotypic screening and molecular profiling.
Sci Rep
December 2024
Bioinformatics Laboratory, Research & Developmental Cell, Parul University, Vadodara, 391760, Gujarat, India.
Finger millet blast caused by Pyricularia grisea hinders crop's growth and is a serious threat to economic yield. It can lead to massive yield losses i.e.
View Article and Find Full Text PDFFirst microsatellite markers for the Amazonian species Copaifera multijuga Hayne developed using next-generation sequencing.
Mol Biol Rep
December 2024
Laboratório de Biologia Molecular (LBM), Centro de Bionegócios da Amazônia (CBA), Manaus, Amazonas, Brazil.
Background: Native to the Amazon region, Copaifera multijuga Hayne is a large tree (≈ 36 m in height) that is heavily exploited for extraction of its oleoresin. Many studies have addressed the phytochemical properties and applications of this raw material; however, there are few initiatives that have focused on the genetic characterization of native populations of this species. To this end, our objective was to develop microsatellite markers for C.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!