Tiwari, V.K., Wang, S., Sehgal, S., Vrána, J., Friebe, B., Kubaláková, M., Chhuneja, P., Doležel, J., Akhunov, E., Kalia, B., Sabir, J., Gill, B.S.
BMC GENOMICS
15:
273,
2014
Keywords:
Abstract:
Background: Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular
mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of
genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm
(5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use
for monitoring alien introgressions in wheat (Triticum aestivum L).
Results: The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was
flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was
amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP
discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were
discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by
Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to
wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for
chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg
translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL ·
5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest
introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines
with Lr57 and Yr40 genes.
Conclusion: This approach should be widely applicable for the identification of species/genome-specific SNPs. The
development of a large number of SNP markers will facilitate the precise introgression and monitoring of alien segments
in crop breeding programs and further enable mapping and cloning novel genes from the wild relatives of crop plants.
Fulltext: contact IEB authors
IEB authors: Jaroslav Doležel,
Marie Kubaláková,
Jan Vrána
Čeština
English