Discovery of genome-wide genetic variations and development of first set of InDel markers for genetics research in cashew

Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB

“…To date, in the majority of the genetic studies in cashew, the first generation or dominant markers, viz., RAPD, ISSR, and AFLP markers, have been used ( Mneney et al., 2001 ; Dhanaraj et al., 2003 ; Archak et al., 2003a ; Archak et al., 2003b ; Archak et al., 2009 ; Thimmappaiah et al., 2009 ; Aliyu, 2012 ; Jena et al., 2016 ; Borges et al., 2018 ; dos Santos et al., 2019 ; da Costa Gomes et al., 2021 ) due to the limited availability of co-dominant markers viz., SSR, SNP and InDel (Insertion/Deletion) markers ( Croxford et al., 2006 ; Savadi et al., 2022a ; Savadi et al., 2023 ). Among the co-dominant markers, microsatellite or SSR markers have gained wide popularity and become markers of choice for genetic studies because of their multi-allelism, high abundance in the genome, ease of use, and amenability for high-throughput analysis ( Taheri et al., 2018 ; Savadi et al., 2020b ).…”

“…Previously, the development of microsatellite or SSR markers was an expensive and time-consuming process. But the rapid improvements in sequencing technologies and bioinformatics have reduced the cost and time required for the development of a large set of robust markers through genome sequencing and in silico mining of the genome sequences for potential markers ( Luo et al., 2021 ; Wang et al., 2022 ; Savadi et al., 2023 ). To date, there have been no studies on the genome-wide characterization of microsatellites or SSRs in cashew.…”