The origin and widespread occurrence of Sli-based self-compatibility in potato.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Corentin R ClotHerman J van Eck

Abstract

Self-compatible (SC) diploid potatoes allow innovative potato breeding. Therefore, the Sli gene, originally described in S. chacoense, has received much attention. In elite S. tuberosum diploids, spontaneous berry set is occasionally observed. We aimed to map SC from S. tuberosum origin. Two full-sib mapping populations from non-inbred diploids were used. Bulks were composed based on both pollen tube growth and berry set upon selfing. After DNA sequencing of the parents and bulks, we generated k-mer tables. Set algebra and depth filtering were used to identify bulk-specific k-mers. Coupling and repulsion phase k-mers, transmitted from the SC parent, mapped in both populations to the distal end of chromosome 12. Intersection between the k-mers from both populations, in coupling phase with SC, exposed a shared haplotype of approximately 1.5 Mb. Subsequently, we screened read archives of potatoes and wild relatives for k-mers specific to this haplotype. The well-known SC clones US-W4 and RH89-039-16, but surprisingly, also S. chacoense clone M6 were positives. Hence, the S. tuberosum source of SC seems identical to Sli. Furthermore, the candidate region drastically reduced to 333 kb. Haplotype-specific KASP markers were designed a...Continue Reading

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Citations

Jun 26, 2021·Cell·Chunzhi ZhangSanwen Huang
Aug 25, 2021·Cell Research·Martin MascherNils Stein
Jul 8, 2021·Nature Communications·Ling MaYi Shang

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Datasets Mentioned

BETA
PRJEB36551
PRJNA362370
ERR033772
ERR033773
SRR5264022
SRR5090798
PRJNA378971

Methods Mentioned

BETA
ubiquitination
genotyping

Software Mentioned

GlistCompare
CoSSA
Trimmomatic
DM
BWA aln
Comparative Subsequence Sets Analysis ( CoSSA )
Mash
bedtools
Glistmaker
Matplotlib

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