Year-end Sale % OFF 
Abstract
Despite several efforts in the last decade toward development of simple sequence repeat (SSR) markers in peanut, there is still a need for more markers for conducting different genetic and breeding studies. With the effort of the International Peanut Genome Initiative, the availability of reference genome for both the diploid progenitors of cultivated peanut allowed us to identify 135,529 and 199,957 SSRs from the A (Arachis duranensis) and B genomes (Arachis ipaensis), respectively. Genome sequence analysis showed uneven distribution of the SSR motifs across genomes with variation in parameters such as SSR type, repeat number, and SSR length. Using the flanking sequences of identified SSRs, primers were designed for 51,354 and 60,893 SSRs with densities of 49 and 45 SSRs per Mb in A. duranensis and A. ipaensis, respectively. In silico PCR analysis of these SSR markers showed high transferability between wild and cultivated Arachis species. Two physical maps were developed for the A genome and the B genome using these SSR markers, and two reported disease resistance quantitative trait loci (QTLs), qF2TSWV5 for tomato spotted wilt virus (TSWV) and qF2LS6 for leaf spot (LS), were mapped in the 8.135 Mb region of chromosome A04 of A. duranensis. From this genomic region, 719 novel SSR markers were developed, which provide the possibility for fine mapping of these QTLs. In addition, this region also harbors 652 genes and 49 of these are defense related genes, including two NB-ARC genes, three LRR receptor-like genes and three WRKY transcription factors. These disease resistance related genes could contribute to resistance to viral (such as TSWV) and fungal (such as LS) diseases in peanut. In summary, this study not only provides a large number of molecular markers for potential use in peanut genetic map development and QTL mapping but also for map-based gene cloning and molecular breeding.
Highlights
Cultivated peanut or groundnut (Arachis hypogaea L.), is a source of high quality edible oil and protein, and is one of the most important oil crops worldwide
The whole genome sequences of A. duranensis and A. ipaensis were downloaded from PeanutBase3
The current trend is more toward using single nucleotide polymorphism (SNP) markers in advanced research organizations in peanut (Pandey et al, 2017), the majority of research organizations with low to moderate genomics facilities still use simple sequence repeat (SSR) in their research
Summary
Cultivated peanut or groundnut (Arachis hypogaea L.), is a source of high quality edible oil and protein, and is one of the most important oil crops worldwide. Significant progress has been made in developing genomic resources which facilitated several successful efforts of trait mapping and molecular breeding in peanut (Pandey et al, 2012, 2016; Varshney et al, 2013). These studies used low density genetic maps and could not provide the optimum level of resolution for trait dissection and discovery of candidate genes. Some of these studies produced very good results despite deploying the minimal genomic and genetic resources including SSRs available at that time (Varshney et al, 2013)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
