Genome-wide discovery of microsatellite markers from diploid progenitor species, Arachis duranensis and A. ipaensis, and their application in cultivated peanut (A. hypogaea)

Authors: ZHAO, CHUANZHI; QIU, JINGJING; AGARWAL, GAURAV; WANG, JIANGSHAN; REN, XUEZHEN; XIA, HAN; Guo, Baozhu; MA, CHANGLE; BERTIOLI, DAVID; VARSHNEY, RAJEEV; PANDEY, MANISH; WANG, XINGJUN

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/26/2017
Publication Date: 7/18/2017
Citation: Zhao, C., Qiu, J., Agarwal, G., Wang, J., Ren, X., Xia, H., Guo, B., Ma, C., Bertioli, D.J., Varshney, R.K., Pandey, M.K., Wang, X. 2017. Genome-wide discovery of microsatellite markers from diploid progenitor species, Arachis duranensis and A. ipaensis, and their application in cultivated peanut (A. hypogaea). Frontiers in Plant Science. 8:1209. https://doi.org/10.3389/fpls.2017.01209.
DOI: https://doi.org/10.3389/fpls.2017.01209

Interpretive Summary: Cultivated peanut, as a source of high quality edible oil and high-quality protein, is one of the most important oil crops worldwide. However, peanut is often grown on marginal soils with lesser inputs and usually intercropped with cereals in many countries. Peanut production and productivity is often constrained by several biotic and abiotic factors, such as drought, salinity, bacterial wilt disease and leaf spot disease. During the past decade, a significant progress has been made in developing optimum genomic resources which facilitated genetic studies successfully for trait mapping and molecular breeding studies in peanut. Nevertheless, genome sequencing has been completed for two diploid progenitors of cultivated peanut. The high quality genome assemblies developed by the International Peanut Genome Initiative (IPGI) and the Peanut Genome Consortium (PGC) provided new opportunity for developing genetic markers from genome-wide structural variations in peanut. As the members of IPGI and the joint effort to accelerate the marker-assisted selection (MAS) in peanut, we identified and developed 135,529 and 199,957 genomic SSRs from both diploid progenitors of cultivated peanuts, respectively. This study also demonstrated high transferability for these SSRs in different Arachis species, indicating high potential for their useful applications in improving cultivated peanut.

Technical Abstract: Despite several efforts in last decade towards development of simple sequence repeat (SSR) markers in peanut, there is still a need of more markers such as SSRs for conducting different genetic and breeding studies. With the effort of International Peanut Genome Initiative, 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 genome (Arachis duranensis) and the B genome (A. ipaensis), respectively. Genome sequence analysis showed uneven distribution of the SSR motifs across genomes such as SSR types, repeat numbers, and SSR length. Using the flanking sequences of identified SSRs, primers were designed for a total of 51,354 and 60,893 SSRs with the densities of 49.13 and 44.98 SSRs per Mb in A. duranensis and A. ipaensis, respectively. In silico PCR analysis, it was demonstrated that these SSR markers showed high transferability between wild and cultivated Arachis species. Two physical maps containing SSR markers were developed for the A genome and the B genome using these SSR markers, and two reported disease resistance QTLs, qF2TSWV5 for Tomato spotted wilt virus (TSWV) and qF2LS6 for leaf spot (LS), were mapped in the region of 8.135 Mb 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 the resistance to this viral disease TSWV and the LS fungal disease 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.