The genetic basis of inbreeding depression in potato

Zhang, Chengqi; Wang, Pei; Tang, Dié; Yang, Zhuo; Lü, Fei; Qi, Jianjian; Tawari, Nilesh R.; Shang, Yi; Li, Canhui; Huang, Sanwen

doi:10.1038/s41588-018-0319-1

Cited by 129 publications

(140 citation statements)

References 26 publications

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“…Except for wv1 ( Supplementary Fig. 14), the other five loci have been previously reported 39 . Here, we relocated these loci on the phased RH genome, clarifying which haplotype contained the dominant or recessive allele (Fig.…”

Section: Letters Nature Geneticsmentioning

confidence: 94%

“…The selfing population (S 1 population, equivalent to an F 2 population) of RH was constructed by forced self-pollination 39 and 880 F 2 individuals were sequenced at ~1× depth using an Illumina HiSeq X Ten platform. On average, ~2 Gb of data were obtained from each individual.…”

Section: Methodsmentioning

confidence: 99%

“…Dots in the graphs present the genetic markers. The ar1 locus has been reported previously39 . c, Fine mapping of ws1 and pa1 using indel markers (green bars).…”

mentioning

confidence: 86%

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Haplotype-resolved genome analyses of a heterozygous diploid potato

et al. 2020

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Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using a combination of multiple sequencing strategies, including circular consensus sequencing. Comparison of the two haplotypes revealed ~2.1% intragenomic diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles via meiotic recombination. This study offers a holistic view of the genome organization of a clonally propagated diploid species and provides insights into technological evolution in resolving complex genomes.

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Section: Letters Nature Geneticsmentioning

confidence: 94%

Section: Methodsmentioning

confidence: 99%

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Haplotype-resolved genome analyses of a heterozygous diploid potato

et al. 2020

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“…The rapid development of diploid hybrid breeding is coupled with the prospects to cardinally shorten the duration of the breeding process and reduce the costs of producing and multiplying healthy clones (Lindhout et al, 2011(Lindhout et al, , 2018De Vries et al, 2016;Jansky et al, 2016), because most of potato pathogens are not transmitted with pollen or TPS. The onset of diploid hybrid breeding called for a need to study genetic bases of self-incompatibility (Phumichai et al, 2005) and inbreeding depression in potato (Zhang et al, 2019) in order to obtain inbred diploid lines, as well as to promote research on male sterility and CMS-Rf genetic systems, aimed at the development of effective interline hybridization techniques (Anisimova, Gavrilenko, 2017). Previously, those challenges have had not been so relevant, so far as the conventional potato production is based on vegetative reproduction of highly heterozygous tetraploid cultivars.…”

Section: Introductionmentioning

confidence: 99%

Cytoplasmic genetic diversity of potato varieties bred in Russia and FSU countries

et al. 2019

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Male sterility in potato is little studied since traditional breeding is based on the vegetative reproduction of highly heterozygous tetraploid varieties. The rapid development of hybrid diploid breeding contributes to growing interest in studying the male sterility of this important crop. In this work, a set of 6 cytoplasmic markers was employed to describe cytoplasmic genetic diversity of 185 potato cultivars bred in Russia and FSU countries. Three cytoplasm types were identified, T (40.0 %), D (50.8 %) and W/γ (8.7 %), which according to literature are associated with male sterility. With a single exception (0.5 %), cytoplasm types characteristic of male fertile forms (A, P) were not found in the subset of 185 cultivars. A comparison of these results with previously published data suggested expanding the subset to up to 277 cultivars, all developed in Russia or FSU countries; however, the resulting differentiation into three cytoplasm types (T, D and W/γ) was nearly the same. Fertility phenotyping helped identify both male-sterile and male-fertile genotypes within the three groups of varieties with T-, D-and W/γ-type cytoplasm. Fifteen genotypes differing in cytoplasm type and male sterility/fertility traits were selected for direct sequencing of 8 mtDNA loci. Fragments of the nad2, nad7, cox2, atp6 and CcmFc genes were identical in all 15 selected genotypes. The polymorphism, detected in the rps3, atp9 and CcmFc loci, was not associated with male sterility. Two SNPs in the nad1/ atp6 and nad2 loci differentiated 7 genotypes with W/γ-type cytoplasm into five genotypes with tetrad sterility, and two with fertile pollen. The results of an NGS analysis confirmed the association of these SNPs with tetrad sterility in a larger set of 28 genotypes of different origin, all with W/γ-type cytoplasm. A heteroplasmy state was observed both in male-sterile and in male-fertile genotypes.

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“…And while many outliers were shared among accessions ( Figure 2B and S8), indicating some shared signal resulting from DH production, the majority of outliers were accession specific. In other crops like potato, it has been shown that the genomic signals of inbreeding are largely specific to individual lines (Zhang et al 2019). The increased strength of selection due to the instantaneous homozygosity during DH production and the shared history of European maize landraces might have caused the increased signal of shared outliers among accessions.…”

Section: Dh Production Creates Selection Hotspotsmentioning

confidence: 99%

Selective loss of diversity in doubled-haploid lines from European maize landraces

Zeitler

Ross‐Ibarra

Stetter

2019

Preprint

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Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in ex-situ programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of inbreeding which results in instantaneous homozygosity genome-wide. Here we analyzed the effect of DH production on genetic diversity, using genome-wide SNP data from hundreds of individuals of five European landraces and their related DH lines. In contrast to previous findings, we observe a dramatic loss of diversity at both the haplotype level and that of individual SNPs. We identify thousands of SNPs that exhibit allele frequency differences larger than expected under models of neutral genetic drift, and document patterns of heterozygosity and polymorphism at conserved sites that suggest an important role for deleterious recessive load in determining diversity differences between landrace and DH populations.Although we were unable to uncover more details about the mode of selection, we conclude that while landrace DH lines may be a valuable tool for the introduction of variation into maize breeding programs they come at the cost of decreased genetic diversity and increased genetic load.

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The genetic basis of inbreeding depression in potato

Cited by 129 publications

References 26 publications

Haplotype-resolved genome analyses of a heterozygous diploid potato

Haplotype-resolved genome analyses of a heterozygous diploid potato

Cytoplasmic genetic diversity of potato varieties bred in Russia and FSU countries

Selective loss of diversity in doubled-haploid lines from European maize landraces

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