Abstract
Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservoir” for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.
Highlights
Crop improvement by breeding relies on genetic variation
Wild rice species and the cultivated rice species belong to the genus Oryza, which consists of two cultivated species, O. sativa (Asian rice) and O. glaberrima (African rice), and 22 wild species representing 11 genome types, of which six are diploid (AA, BB, CC, EE, FF, and GG) and five are allotetraploid (BBCC, CCDD, HHJJ, HHKK, and KKLL)[14,15]
The chromosome levels of whole-genome sequences of AA-genome wild species and indica cultivars were obtained from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/) with GenBank accession numbers: O. nivara (PRJNA48107), O. barthii (PRJNA30379), O. glumaepatula (PRJNA48429), and O. meridionalis (PRJNA48433), which were submitted by the International Oryza Map Alignment Project (IOMAP)[40]; Minghui 63 (PRJNA302543) and Zhenshan 97 (PRJNA302542) submitted by Zhang et al.[41]; and IR8 (PRJNA353946) submitted by Stein et al.[16]
Summary
Crop improvement by breeding relies on genetic variation. Domestication processes from wild progenitors and repeated use of elite germplasm in breeding programs narrowed down the genetic v ariation[1,2]. An interspecific hybridization between the cultivated species and wild species was conducted for the selection of improved lines for breeding purposes and the identification of the QTLs/genes governing important agronomic traits by applying genetics and molecular genomics tools. As consequences of those efforts, the DNA of wild species knowingly and unknowingly contributed a lot to rice improvement such as for biotic stress resistance, abiotic stress tolerance, and grain yield. The information produced in this study will provide groups of marker sets consisting of the potential polymorphic markers between indica and specific AA-genome species as well as between japonica and specific AA-genome species
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