bims-plasge Biomed News
on Plastid genes
Issue of 2020‒01‒26
three papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

  1. PLoS One. 2020 ;15(1): e0227148
      We used genotyping-by-sequencing (GBS) to investigate the evolutionary history of domesticated tetraploid wheats. With a panel of 189 wild and domesticated wheats, we identified 1,172,469 single nucleotide polymorphisms (SNPs) with a read depth ≥3. Principal component analyses (PCAs) separated the Triticum turgidum and Triticum timopheevii accessions, as well as wild T. turgidum from the domesticated emmers and the naked wheats, showing that SNP typing by GBS is capable of providing robust information on the genetic relationships between wheat species and subspecies. The PCAs and a neighbour-joining analysis suggested that domesticated tetraploid wheats have closest affinity with wild emmers from the northern Fertile Crescent, consistent with the results of previous genetic studies on the origins of domesticated wheat. However, a more detailed examination of admixture and allele sharing between domesticates and different wild populations, along with genome-wide association studies (GWAS), showed that the domesticated tetraploid wheats have also received a substantial genetic input from wild emmers from the southern Levant. Taking account of archaeological evidence that tetraploid wheats were first cultivated in the southern Levant, we suggest that a pre-domesticated crop spread from this region to southeast Turkey and became mixed with a wild emmer population from the northern Fertile Crescent. Fixation of the domestication traits in this mixed population would account for the allele sharing and GWAS results that we report. We also propose that feralization of the component of the pre-domesticated population that did not acquire domestication traits has resulted in the modern wild population from southeast Turkey displaying features of both the domesticates and wild emmer from the southern Levant, and hence appearing to be the sole progenitor of domesticated tetraploids when the phylogenetic relationships are studied by methods that assume a treelike pattern of evolution.
  2. Mol Plant. 2020 Jan 18. pii: S1674-2052(20)30005-8. [Epub ahead of print]
      Speciation has long been regarded as an irreversible process once the reproductive barriers had been established. However, unlike in natural populations, artificial selection might either accelerate or prevent speciation processes in domesticated species. Asian cultivated rice is a target crop for both domestication and artificial breeding; it contains two subspecies of indica and japonica, which usually produce sterile inter-subspecific hybrids due to reproductive barriers. Here we constructed the evolutionary trajectory of a reproductive isolation system S5, which regulates fertility in indica-japonica hybrids via three adjacent genes, based on data of 606 accessions including two cultivated and 11 wild rice species. Although hybrid sterility haplotypes at S5 led to establishment of a killer-protector reproductive barrier, origin of wide-compatibility haplotypes by complex hybridization and recombination provided an opposing force to reproductive isolation and thus prevented speciation during domestication. Analysis in a diallel set of 209 crosses involving 21 parents showed that the wide-compatibility genotypes largely reduced sterility of indica-japonica hybrids indicating that wide compatibility gene would enable gene flow to maintain species coherence. This counter-acting system indicates that combined effects of natural evolution and artificial selection may result in reversible processes of speciation in rice, which may also have implications for rice genetic improvement.
    Keywords:  Oryza sativa L.; artificial selection; hybrid sterility; reproductive isolation; reversible; speciation; wide-compatibility
  3. Theor Appl Genet. 2020 Jan 22.
      KEY MESSAGE: The yellow margin (ym) gene was mapped to a 30-kb genomic region in potato and the mutation of a pectate lyase gene led to this phenotype. The practice of clonally propagating potato (Solanum tuberosum L.), which has been lasted for thousands of years, has caused the accumulation of deleterious alleles. Despite yellow margin (ym) being a common cause of a detrimental weak-vigor phenotype and reduced yield in diploid potato, the underlying gene has eluded discovery to date. In this paper, we mapped the ym gene to a 30-kb region containing four annotated genes. Among them, PGSC0003DMG402023481 encodes a pectate lyase-like gene (StPLL) with lower expression in ym plants than in the wild-type plants. PCR amplification confirmed a 4.1-kb deletion in the mutant allele of StPLL. Knockout of StPLL in diploid potato resulted in a similar phenotype with the ym plants. This study not only characterizes the ym allele but also provides the molecular tools to select and purge it from populations, while also deepening our understanding of the morphogenesis in potato.