Linkage Analysis and QTL Mapping Using SNP Dosage Data in a Tetraploid Potato Mapping Population

Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930–932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30–40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping.

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Identification and QTL mapping of resistance to Turnip yellows virus (TuYV) in oilseed rape, Brassica napus

Theoretical and Applied Genetics ◽

10.1007/s00122-019-03469-z ◽

2019 ◽

Vol 133 (2) ◽

pp. 383-393 ◽

Cited By ~ 3

Author(s):

Dieter Hackenberg ◽

Elvis Asare-Bediako ◽

Adam Baker ◽

Peter Walley ◽

Carol Jenner ◽

...

Keyword(s):

Brassica Napus ◽

Qtl Mapping ◽

Oilseed Rape ◽

Genetic Resource ◽

Mapping Population ◽

Resistant Parent ◽

Potato Aphid ◽

Turnip Yellows Virus ◽

Peach Potato Aphid ◽

Major Qtl

Abstract Key message Partially dominant resistance to Turnip yellows virus associated with one major QTL was identified in the natural allotetraploid oilseed rape cultivar Yudal. Abstract Turnip yellows virus (TuYV) is transmitted by the peach-potato aphid (Myzus persicae) and causes severe yield losses in commercial oilseed rape crops (Brassica napus). There is currently only one genetic resource for resistance to TuYV available in brassica, which was identified in the re-synthesised B. napus line ‘R54’. In our study, 27 mostly homozygous B. napus accessions, either doubled-haploid (DH) or inbred lines, representing a diverse subset of the B. napus genepool, were screened for TuYV resistance/susceptibility. Partial resistance to TuYV was identified in the Korean spring oilseed rape, B. napus variety Yudal, whilst the dwarf French winter oilseed rape line Darmor-bzh was susceptible. QTL mapping using the established Darmor-bzh × Yudal DH mapping population (DYDH) revealed one major QTL explaining 36% and 18% of the phenotypic variation in two independent experiments. A DYDH line was crossed to Yudal, and reciprocal backcross (BC1) populations from the F1 with either the susceptible or resistant parent revealed the dominant inheritance of the TuYV resistance. The QTL on ChrA04 was verified in the segregating BC1 population. A second minor QTL on ChrC05 was identified in one of the two DYDH experiments, and it was not observed in the BC1 population. The TuYV resistance QTL in ‘R54’ is within the QTL interval on Chr A04 of Yudal; however, the markers co-segregating with the ‘R54’ resistance are not conserved in Yudal, suggesting an independent origin of the TuYV resistances. This is the first report of the QTL mapping of TuYV resistance in natural B. napus.

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