Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01

Abstract

BackgroundA landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, the genome positions of these markers need to be mapped.ResultsTwo high density genetic linkage maps were constructed based on 21,478 single nucleotide polymorphism loci mapped in the Williams 82 x G. soja (Sieb. & Zucc.) PI479752 population with 1083 RILs and 11,922 loci mapped in the Essex x Williams 82 population with 922 RILs. There were 37 regions or single markers where marker order in the two populations was in agreement but was not consistent with the physical position in the Glyma1.01 build. In addition, 28 previously unanchored scaffolds were positioned. Map data were used to identify false joins in the Glyma1.01 assembly and the corresponding scaffolds were broken and reassembled to the new assembly, Wm82.a2.v1. Based upon the plots of the genetic on physical distance of the loci, the euchromatic and heterochromatic regions along each chromosome in the new assembly were delimited. Genomic positions of the commonly used markers contained in BARCSOYSSR_1.0 database and the SoySNP50K BeadChip were updated based upon the Wm82.a2.v1 assembly.ConclusionsThe information will facilitate the study of recombination hot spots in the soybean genome, identification of genes or quantitative trait loci controlling yield, seed quality and resistance to biotic or abiotic stresses as well as other genetic or genomic research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2344-0) contains supplementary material, which is available to authorized users.

Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

“…However, the recent advancement in next generation sequencing technology has provided an affordable platform for studying genome-wide variation in watermelon populations leading to the development of genetic maps of sufficient genome coverage (Cheng et al, 2016;Sandlin et al, 2012;Ren et al, 2012), including a consensus map based on 386 SNPs, 698 simple sequence repeats, 219 insertiondeletion and 36 structure variation markers (Ren et al, 2014). However, the marker-density in these maps is low compared to major crops such as maize (Zea mays) (1.15 million markers, Liu et al, 2015), soybean (Glycine max) (21,478 markers, Song et al, 2016), wheat (Triticum aestivum) (30,144 markers, Maccaferri et al, 2015) and rice (Oryza sativa) (30,984 markers, Spindel et al, 2013). Genotyping by sequencing (GBS) (Elshire et al, 2011) is a highly multiplexed next-generation sequencing technology that can generate thousands of markers in any plant species and involves sequencing of reduced genomic libraries followed by alignment of the generated reads to identify SNP variations (Barba et al, 2014;Elshire et al, 2011).…”

Whole‐genome re‐sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad‐based resistance to soybean cyst nematode

“…None of the elite lines carry multiple copies at the Rhg4 locus and most of the lines (49/ 57) were highly susceptible to two or more SCN races (Table S4). To further confirm this result we utilized the whole-genome sequence and CGH data from soybean NAM (Nested Association Mapping) population (Song et al, 2017) (https://www.soybase. org/SoyNAM/) and estimated CNV (Anderson et al, 2014) (Table S7).…”

“…The gene Glyma.08g108900, encoding Serine hydroxymethyltransferase ( GmSHMT08 ), showed three non‐synonymous SNPs associated with the SCN reaction (Figure ). In the earlier soybean reference genome assembly W82.a1, GmSHMT08 (alias Glyma08g11490 ) was predicted to produce 503 amino acids, whereas in the most current assembly W82.a2 (Song et al ., ) the primary transcript was 573 amino acids long. The first 70 amino acids in the assembly W82.a1 were missing, and this could be caused by an alternative splicing event or exon skipping.…”

A high‐resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance

“…Accurate genetic maps are essential for the mapping of complex traits (e.g. Wang et al, 2015;Zhou et al, 2016) and for the validation and improvement of genomic sequence assemblies (Paux et al, 2008;Bartholom e et al, 2015;Silva-Junior and Grattapaglia, 2015;Song et al, 2016). In wheat, an ultra-highdensity and accurate reference genetic map has also enabled to identify genomic blocks with segregation distortion and segments of introgression (Gardner et al, 2016).…”

“…Genetic mapping has recently been used in several projects to position gene coding regions on plant genomes and help build physical genome maps to anchor sequence scaffolds obtained from WGS, e.g. in chickpea (Deokar et al, 2014), melon (Argyris et al, 2015), potato (Xu et al, 2011), ryegrass (Velmurugan et al, 2016), and soybean (Song et al, 2016). Mapping population sequencing and genetic mapping also enabled the generation of more contiguous genome sequence assembly for barley, wheat and sesame genomes (Mascher et al, 2013;Chapman et al, 2015;Wang et al, 2016).…”