Genome architecture and tetrasomic inheritance of autotetraploid potato

Desynapsis in potato is caused byStMSH4mutant alleles and leads to either highly uniform unreduced pollen or sterility

“…A local blast database was build using Nucleotide-Nucleotide BLAST 2.8.1+ (Camacho et al 2009) with a S. lycopersicum cv. Heinz 170 build SL5.0 genome (Zhou et al 2022) and 18 de-novo assembled potato genomes: M6 v.4.1 (Leisner et al 2018); DM v.6.1 (Pham et al 2020); Solyntus v.1.1 (van Lieshout et al 2020); RH89-039-16 v.3 (Zhou et al 2020); A6-26, E4-63, E86-69, PG5068, PG6359 and PG0019 (Tang et al 2022) ; Atlantic v.2.0, Castle Russet v.2.0, Avenger, Atlus, Columba and, Spunta (Hoopes et al 2022); Otava v.1 (Sun et al 2022); C88 v.1 (Bao et al 2022). The genomic sequence of Soltu.DM.08G000640 ( StMSH4 in DM v.6.1) was used as query and the results were manually curated to stitch together partial hits within 5-kb of each other, assumed to be truncated by structura l variations.…”

Why 2022 is a revolutionary year for potato genomics

“…Spotlight to exhibit differential expression, meaning that some copies were actively producing proteins and contributing to the work of running the organism, while others were more or less dormant. Bao et al (2022), for example, estimated that while about half the genes they surveyed were expressed at significantly different levels from different copies of the genome, there did not appear to be any tendency for genes on a particular copy to dominate (Figure 1). The lack of any dominant genome explains why deleterious mutation has occurred significantly across all four copies of the genome, and the remaining functional copies of these decrepit genes also occur across all the copies.…”

“…The concept shows great promise and will benefit greatly from genome resources, especially broad surveys of diploid varieties, such as the wild and cultivated diploids assembled by Tang et al (2022). Indeed, the ability of wild potato genetic material to contribute to desirable cultivated potatoes is underscored by some of the work done on the evolutionary histories of the 2022 tetraploid genomes (Bao et al, 2022;Hoopes et al, 2022), showing that wild species have contributed liberally to the cultivated genome in the past, in one case even contributing an entire half-chromosome. All these potato genome resources combined with new breeding methods like those reported by Zhang et al (2021) will accelerate the breeding of stronger, healthier, and more environmentally resilient potato varieties with all the qualities that make them a beloved staple of so many cuisines across the globe.…”

“…The process of inferring what sequence belongs to what haplotype is known as phasing, and the challenge of phasing a complete tetraploid genome remained effectively impossible until long-range, high-accuracy DNA sequencing coupled with algorithmic advances helped to overcome the challenges in very recent times. This year, two studies published in Molecular Plant (Bao et al, 2022;Hoopes et al, 2022) along with one published in Nature Genetics (Sun et al, 2022) finally reported fully phased whole-genome assemblies of, in the case of Hoopes et al (2022), up to six tetraploid potato cultivars. The comparative ease of assembling diploid genomes without performing full phasing is perhaps best exemplified by the work of Tang et al (2022), who added significantly to the 2022 potato genome boom when releasing 44 wild and cultivated diploid genome assemblies in a single study.…”

“…An important component of genomics-assisted breeding is the detection of undesirable mutations. Since potentially destructive (or deleterious) mutations can be detected with some confidence (Cingolani et al, 2012), both Hoopes et al (2022) and Bao et al (2022) were able to employ an algorithm to automatically tabulate many such mutations, and Sun et al (2022) even calculated that, in the case of almost half the genes of the variety 'Otava', mutation had been so severe as to effectively eliminate one or more copies of the gene. Accumulating mutations does not always indicate functional decay.…”