Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius)

BMC Genomics
Huaan YangChengdao Li

Abstract

Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding. Nine lupin cultivars released in Australia from 1973 to 2007 were subjected to whole genome re-sequencing. The re-sequencing data together with the reference genome sequence data were used in marker development, which revealed 180,596 to 795,735 SNP markers from pairwise comparisons among the cultivars. A total of 207,887 markers were anchored on the lupin genetic linkage map. Marker mining obtained an average of 387 SNP markers and 87 InDel markers for each of the 24 genome sequence assembly scaffolds bearing markers linked to 11 genes of agronomic interest. Using the R gene PhtjR conferring resistance to phomopsis stem blight disease as a test case, we discovered 17 candidate diagnostic markers by genotyping and selecting markers on a g...Continue Reading

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Citations

May 12, 2016·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Katarzyna WyrwaBarbara Naganowska
Oct 21, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Gaofeng ZhouHuaan Yang
Sep 25, 2020·Journal of Applied Genetics·Sandra Rychel-BielskaMichał Książkiewicz
Jan 13, 2021·International Journal of Molecular Sciences·Michał KsiążkiewiczPaweł Krajewski

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Datasets Mentioned

BETA
PRJNA179231
d
AOCW01145302

Methods Mentioned

BETA
Genotyping
PCR
electrophoresis

Software Mentioned

SOAPindel
SOAPsnp
Blast search
MapManager QTX
circus
MAS
MapManager
BLAST
SOAPdenovo
LightScanner

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