A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome.
Bottom Line: Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both the maternal and paternal parents.The alfalfa linkage groups were highly syntenous with M. truncatula, and clearly identified the known translocation between Chromosomes 4 and 8.GBS could be used in breeding populations to accelerate molecular breeding in alfalfa.
Affiliation: Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401.Show MeSH
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Mentions: A high level of synteny was observed between the alfalfa linkage maps and the M. truncatula physical map using a cutoff E-value of < 1 × 10−5 (Figure 3, Figure 4, and Figure 5 and Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, and Figure S7). Using either Bowtie or BLAST with a more stringent cutoff E-value < 1 × 10−20, resulted in fewer SNP markers aligning to unmatching chromosomes of the M. truncatula reference genome (Figure 3 and Figure 4). This indicated that most of the noise observed using the less stringent cutoff was from the unreliable alignment of SNP markers to M. truncatula reference genome. A reciprocal translocation between Chromosomes 4 (at 37−39 Mbp) and 8 (at 33−35 Mbp) was identified (Figure S3, Figure S7, and Table S3). An inversion on Chromosome 1 was observed between the M. truncatula physical map and all four haplotype maps of DM5 and two haplotype maps of DM3 (Figure 5). The remaining two DM3 haplotype maps did not have sufficient marker density to identify whether the inversion was present.
Affiliation: Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401.