Assessing the Contribution of Sli to Self-Compatibility in North American Diploid Potato Germplasm Using KASP™ Markers

Kaiser, Natalie; Jansky, Shelley; Coombs, Joseph; Collins, Paul J.; Alsahlany, Maher; Douches, David S.

doi:10.1007/s12230-021-09821-8

Cited by 14 publications

(21 citation statements)

References 39 publications

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“…Genotyping of the Sli locus on chromosome 12 using Kompetitive Allele Specific PCR (KASP)™ markers was conducted with genomic DNA from the nine diploid clones using the methods described by Clot et al (2020) . KASP markers ST4_03ch12 58962561 and ST4_03ch12 59040898 were used and assays were run according to Kaiser et al (2021) on a Light Cycler 480 Real-Time PCR system (Roche, Germany). The 3.25 μl reaction system with 1.5 μl v4.0 2× Low ROX KASP Mastermix (LGC Genomics, Beverly, MA, United States), 0.05 μl KASP Assay by Design primer and 1.7 μl of 15–10 ng/μl genomic DNA was used.…”

Section: Methodsmentioning

confidence: 99%

Genome sequencing of adapted diploid potato clones

et al. 2022

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Cultivated potato is a vegetatively propagated crop, and most varieties are autotetraploid with high levels of heterozygosity. Reducing the ploidy and breeding potato at the diploid level can increase efficiency for genetic improvement including greater ease of introgression of diploid wild relatives and more efficient use of genomics and markers in selection. More recently, selfing of diploids for generation of inbred lines for F1 hybrid breeding has had a lot of attention in potato. The current study provides genomics resources for nine legacy non-inbred adapted diploid potato clones developed at Agriculture and Agri-Food Canada. De novo genome sequence assembly using 10× Genomics and Illumina sequencing technologies show the genome sizes ranged from 712 to 948 Mbp. Structural variation was identified by comparison to two references, the potato DMv6.1 genome and the phased RHv3 genome, and a k-mer based analysis of sequence reads showed the genome heterozygosity range of 1 to 9.04% between clones. A genome-wide approach was taken to scan 5 Mb bins to visualize patterns of heterozygous deleterious alleles. These were found dispersed throughout the genome including regions overlapping segregation distortions. Novel variants of the StCDF1 gene conferring earliness of tuberization were found among these clones, which all produce tubers under long days. The genomes will be useful tools for genome design for potato breeding.

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Section: Methodsmentioning

confidence: 99%

Genome sequencing of adapted diploid potato clones

et al. 2022

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“…Kaiser et al. (2021) recently described several SC clones from diverse genetic backgrounds lacking dominant Sli alleles. Candidate genes encoding high‐top protein (Goldraij et al., 2006) (chromosome 12), 120‐kD glycoprotein (Lee et al., 2009) (chromosome 8), and Kunitz‐type proteinase inhibitors (NaStEP) (Jiménez‐Durán et al., 2013) (chromosome 3) have been proposed to modulate the strength of the SC response in Solanum .…”

Section: Discussionmentioning

confidence: 99%

“…(2020) within a candidate Sli region on chromosome 12. The dominant homozygous genotype ( Sli/Sli ) at these two marker loci is significantly associated with self‐compatibility in diverse diploid potato backgrounds (Kaiser et al., 2021). Each KASP assay is composed of an allele‐specific SC and SI forward primer and a common reverse primer (Supplemental Table S4).…”

Section: Methodsmentioning

confidence: 99%

Self‐fertility and resistance to the Colorado potato beetle (Leptinotarsa decemlineata) in a diploid Solanum chacoense recombinant inbred line population

et al. 2021

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A diploid potato (Solanum tuberosum L.) recombinant inbred line population was derived from a cross between Solanum chacoense inbred line M6 and S. chacoense accession USDA8380‐1 (80‐1) to identify loci associated with self‐compatibility and Colorado potato beetle resistance. Individuals from the F4 and F5 generations were genotyped on the Illumina Infinium V3 22K Single Nucleotide Polymorphism (SNP) Array and a genetic map constructed. All F5 individuals contain at least one copy of the dominant S‐locus inhibitor (Sli) haplotype; however, not all F5 individuals set fruit. Pollen tubes reached the ovaries of both self‐fruitful and self‐unfruitful plants, indicating that the presence of the dominant Sli allele is not sufficient for selfed fruit and seed production. Loci on chromosomes 3, 5, 6, and 12 were identified as novel targets for self‐fertility improvement. Evaluation of fruit and seed set upon selfing in the F4 generation over two greenhouse seasons revealed environmental influence on self‐fertility. Loci exhibiting residual heterozygosity were found on all chromosomes except chromosomes 3 and 11 in F5 inbreds, but none of the measured self‐fertility traits were correlated with the level of heterozygosity based on SNP genotyping. Four SNPs on chromosome 2 between 22,151,711 and 22,381,719 bp were associated with foliar leptine glycoalkaloid synthesis and Colorado potato beetle resistance in the recombinant inbred line population. Robust inbred lines carrying Colorado potato beetle resistance were developed without field selection during the inbreeding process and beetle resistance was introgressed into diploid breeding lines.

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“…Clone M6 is widely used as donor for introgression SC. It has been found to be homozygous for six DNA KASP markers (Sli_090, Sli_561, Sli_304, Sli_626, Sli_898, and Sli_424), linked to Sli in Dutch germplasm and spanning a 224 kb region [ 29 ].…”

Section: Molecular Approaches To Overcome Simentioning

confidence: 99%

“…This analysis shows that the SC haplotype is widespread among the tetraploid varieties, and the one selected for dihaploid induction must contain Sli . Interestingly, KASP assays have found Sli in the dihaploids of potato cultivars ‘Atlantic’, ‘Superior’, and the breeding clone NY148 [ 29 ]. This shows that the diploid SC gene pool can be readily expanded without Sli introgression.…”

Section: Sli Gene Identification and Its Functionmentioning

confidence: 99%

Molecular Approaches to Overcome Self-Incompatibility in Diploid Potatoes

Kardile

Yilma

Sathuvalli

2022

Plants

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There has been an increased interest in true potato seeds (TPS) as planting material because of their advantages over seed tubers. TPS produced from a tetraploid heterozygous bi-parental population produces non-uniform segregating progenies, which have had limited uniformity in yield and quality in commercial cultivation, and, thus, limited success. Inbreeding depression and self-incompatibility hamper the development of inbred lines in both tetraploid and diploid potatoes, impeding hybrid development efforts. Diploid potatoes have gametophytic self-incompatibility (SI) controlled by S-locus, harboring the male-dependent S-locus F-box (SLF/SFB) and female-dependent Stylar-RNase (S-RNase). Manipulation of these genes using biotechnological tools may lead to loss of self-incompatibility. Self-compatibility can also be achieved by the introgression of S-locus inhibitor (Sli) found in the self-compatible (SC) natural mutants of Solanum chacoense. The introgression of Sli through conventional breeding methods has gained much success. Recently, the Sli gene has been cloned from diverse SC diploid potato lines. It is expressed gametophytically and can overcome the SI in different diploid potato genotypes through conventional breeding or transgenic approaches. Interestingly, it has a 533 bp insertion in its promoter elements, a MITE transposon, making it a SC allele. Sli gene encodes an F-box protein PP2-B10, which consists of an F-box domain linked to a lectin domain. Interaction studies have revealed that the C-terminal region of Sli interacts with most of the StS-RNases, except StS-RNase 3, 9, 10, and 13, while full-length Sli cannot interact with StS-RNase 3, 9, 11, 13, and 14. Thus, Sli may play an essential role in mediating the interactions between pollen and stigma and function like SLFs to interact with and detoxify the S-RNases during pollen tube elongation to confer SC to SI lines. These advancements have opened new avenues in the diploid potato hybrid.

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Assessing the Contribution of Sli to Self-Compatibility in North American Diploid Potato Germplasm Using KASP™ Markers

Cited by 14 publications

References 39 publications

Genome sequencing of adapted diploid potato clones

Genome sequencing of adapted diploid potato clones

Self‐fertility and resistance to the Colorado potato beetle (Leptinotarsa decemlineata) in a diploid Solanum chacoense recombinant inbred line population

Molecular Approaches to Overcome Self-Incompatibility in Diploid Potatoes

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