Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)

Abstract

BackgroundGenetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics.ResultsIn this study, a wide population consisting of 128 CSSLs was developed, derived from the crossing and back-crossing of two sequenced rice cultivars: 9311, an elite indica cultivar as the recipient and Nipponbare, a japonica cultivar as the donor. First, a physical map of the 128 CSSLs was constructed on the basis of estimates of the lengths and locations of the substituted chromosome segments using 254 PCR-based molecular markers. From this map, the total size of the 142 substituted segments in the population was 882.2 Mb, was 2.37 times that of the rice genome. Second, every CSSL underwent high-throughput genotyping by whole-genome re-sequencing with a 0.13× genome sequence, and an ultrahigh-quality physical map was constructed. This sequencing-based physical map indicated that 117 new segments were detected; almost all were shorter than 3 Mb and were not apparent in the molecular marker map. Furthermore, relative to the molecular marker-based map, the sequencing-based map yielded more precise recombination breakpoint determination and greater accuracy of the lengths of the substituted segments, and provided more accurate background information. Third, using the 128 CSSLs combined with the bin-map converted from the sequencing-based physical map, a multiple linear regression QTL analysis mapped nine QTLs, which explained 89.50% of the phenotypic variance for culm length. A large-effect QTL was located in a 791,655 bp region that contained the rice 'green revolution' gene.ConclusionsThe present results demonstrated that high throughput genotyped CSSLs combine the advantages of an ultrahigh-quality physical map with high mapping accuracy, thus being of great potential value for gene discovery and genetic mapping. These CSSLs may provide powerful tools for future whole genome large-scale gene discovery in rice and offer foundations enabling the development of superior rice varieties.

Highly efficient genomics-assisted development of a library of introgression lines of Solanum pimpinellifolium

“…The rest of the population was completed as follows: 38 BC 3 S 2 ILs, 9 BC 4 S 1 ILs, and 2 BC 3 S 3 ILs. In summary, four ILs were developed in the fifth generation, 47 ILs in the sixth generation, and two ILs in the seventh generation, i.e., overall, a lower number of generations were needed than in other similar works, such as the seven generations needed by Schmalenbach et al (2011) in oats, 8-10 generations by Eshed and Zamir (1994) to develop S. pennellii ILs, 7-10 generations Mol Breeding used by Xu et al (2010) in rice, or nine generations needed by Finkers et al (2007) in tomato. No major problems in marker segregation, fertility, or plant vigor were observed in most families except in two cases.…”

“…Also, additional rounds of high-throughput genotyping are desirable in order to control the genetic background more efficiently. This strategy would not only increase the quality of the introgression line library but also reduce the time for its development, i.e., in the current report, most ILs were developed from a BC 3 S 1 generation (a total of four generations), whereas other populations needed a larger number of generations, such as the 10 generations needed by Eshed and Zamir (1994), nine by Xu et al (2010), seven by Schmalenbach et al (2011), or five by Eduardo et al (2005). Solanum pimpinellifolium germplasm contains genetic variability that obviously cannot be represented in a single IL collection like the current one (Online Resource 2, Blanca et al 2012).…”

“…On the other hand, monitoring genetic backgrounds with genetic markers at medium density, even though it certainly reduces the number of non-target introgressions, does not prevent a certain level of non-isogenity. For example, Xu et al (2010) developed a library of 128 rice introgression lines, finding 117 non-target introgressions, with 50 % of the population having two or more non-target introgressions that were not detected previously, using markers with an average density of 1.6 Mb/marker. Similarly, Schmalenbach et al (2011) found that 76 % of their barley ILs contained one to four additional previously undetected introgressions after high-throughput genotyping.…”

Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare

“…Furthermore, genotyping CSSLs with such low-density markers has a high possibility of missing small introgression segments. The new genotyping method, sequencing-based genotyping, can solve this problem (Huang et al, 2009;Xu et al, 2010). This method is a high-throughput genotyping method that uses SNPs detected by whole-genome resequencing.…”

Emerging Knowledge from Genome Sequencing of Crop Species

“…Overview of projects to study biodiversityCropResults Refs Rice 100 Mb fraction of the Nipponbare reference genome has been analyzed by re-sequencing microarrays within 20 varieties and landraces[94] About 160,000 high-quality SNPs have been discoveredGenome variation maps containing about 8.4 million SNPs has been developed Rice 128 CSSLs, derived from the crossing and back-crossing of two sequenced rice cultivars, have been genotyped in an highthroughput manner by whole genome re-sequencing[119] An physical map of ultrahigh-density SNPs was developedMaizeHapMap was built thanks to re-sequencing of the 27 founders of the NAM population (*135,000 meiotic crossovers)[90] Maize Re-sequencing of 30 random IDSRs (between Palomero and B73 sequenced genomes) across the genome in 16 Mexican landraces and 11 Balsas teosinte accessions[109] …”