Abstract
Wheat leaf rust, caused by the fungus Puccinia triticina Eriks. (Pt), is a destructive disease found throughout common wheat production areas worldwide. At its adult stage, wheat cultivar Liaochun10 is resistant to leaf rust and the gene for that resistance has been mapped on chromosome 2BS. It was designated LrLC10 and is the same gene as cataloged gene Lr13 by pedigree analysis and allelism test. We fine-mapped it using recessive class analysis (RCA) of the homozygous susceptible F2 plants derived from crosses using Liaochun10 as the resistant, male parent. Taking advantage of the re-sequencing data of Liaochun10 and its counterpart susceptible parent, we converted nucleotide polymorphisms in the LrLC10 interval between the resistant and susceptible parents into molecular markers to saturate the LrLC10 genetic linkage map. Four indel markers were added in the 1.65 cM map of LrLC10 flanked by markers CAUT163 and Lseq22. Thirty-two recombinants were identified by those two markers from the 984 F2 homozygous susceptible plants and were further genotyped with additional ten markers. LrLC10 was finally placed in a 314.3 kb region on the Chinese Spring reference sequence (RefSeq v1.0) that contains three high confidence genes: TraesCS2B01G182800, TraesCS2B01G182900, and TraesCS2B01G183000. Sequence analysis showed several variations in TraesCS2B01G182800 and TraesCS2B01G183000 between resistant and susceptible parents. One KASP marker and an indel marker were designed based on the differences in those two genes, respectively, and were validated to be diagnostic co-segregating markers for LrLC10. Our results both improve marker-assisted selection and help with the map-based cloning of LrLC10.
Highlights
Common wheat (Triticum aestivum) is one of the most commonly cultivated crops, comprising 20% of human caloric intake and 15% of cultivated area in the world (FAOSTAT, 2015; WAP, 2017)
We developed molecular markers that were closely linked to LrLC10 and that can be used to facilitate marker-assisted selection of LrLC10 in wheat resistance breeding
The sequences of all the markers anchored in the LrLC10 (Lr13) genetic linkage map were used as queries to search against the Chinese Spring reference genome sequence (RefSeq v1.0) to define the genome interval of the resistance gene on chromosome arm 2BS
Summary
Common wheat (Triticum aestivum) is one of the most commonly cultivated crops, comprising 20% of human caloric intake and 15% of cultivated area in the world (FAOSTAT, 2015; WAP, 2017). Compared with other kinds of markers, kompetitive allele-specific PCR (KASP) assays accelerate the conversion of DNA variations into available gene-linked markers Taking advantage of such whole genomic sequences, Wu et al (2018b) mapped wheat yellow rust resistance gene Yr26 on a 0.003-cM interval on chromosome 1B near the centromere, Narang et al (2019) defined wheat leaf rust resistance gene LrP and yellow rust resistance gene YrP on a 15.71 Mb region on 5DS in the CS RefSeq v1.0 genome assembly, and Wu et al (2019) localized the Pm52 locus within a 5.6 Mb interval on the long arm of chromosome 2B (2BL). We confirmed that the leaf rust resistance gene LrLC10 in Liaochun is Lr13 by pedigree analysis, and finely mapped it to a close interval with recessive class analysis (RCA) through the markers developed according to the resequencing data of the parental lines. We developed molecular markers that were closely linked to LrLC10 and that can be used to facilitate marker-assisted selection of LrLC10 in wheat resistance breeding
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