Multilocus Genotypes of the Wheat Leaf Rust Fungus Puccinia triticina in Worldwide Regions Indicate Past and Current Long-Distance Migration

Many plant pathogenic fungi have a global distribution across diverse ecological zones and agricultural production systems. Puccinia triticina, the wheat leaf rust fungus, is a major pathogen in many wheat production areas of the world. The objective of this research was to determine the genetic relatedness of P. triticina in different worldwide regions. A total of 831 single-uredinial isolates collected from 11 regions were characterized for multilocus genotype at 23 simple sequence repeat loci and for virulence to 20 lines of wheat with single genes for leaf rust resistance. A total of 424 multilocus genotypes and 497 virulence phenotypes were found. All populations had high heterozygosity and significant correlation between virulence and molecular variation, which indicated clonal reproduction. The populations from North America and South America, Central Asia and Russia, and the Middle East and Europe were closely related for multilocus genotypes and many individual isolates from other continental regions were closely related. Twenty-seven multilocus genotypes were found in more than one continental region, and 13 of these had isolates with identical virulence phenotypes. The wide geographic distribution of identical and highly related multilocus genotypes of P. triticina indicated past and more recent migration events facilitated by the spread of clonally produced urediniospores.

Probabilities of multilocus genotypes in SIB recombinant inbred lines

ABSTRACTRecombinant Inbred Lines (RILs) are obtained through generations of inbreeding until all alleles are fixed. In 1931 Haldane and Waddington published a landmark paper where they provided the probabilities of achieving any combination of alleles in 2-way RILs for 2 and 3 loci. In the case of SIB RILs where sisters and brothers are crossed at each generation, there has been no progress in treating 4 or more loci, a limitation we overcome here without much increase in complexity. In the general situation of L loci, the task is to determine 2L probabilities, but we find that it is necessary to first calculate the 4L “identical by descent” (IBD) probabilities that a RIL inherits at each locus its DNA from one of the four originating chromosomes. We show that these 4L probabilities satisfy a system of linear equations that follow from self consistency. In the absence of genetic interference – crossovers arising independently –, the associated matrix can be written explicitly in terms of the recombination rates between the different loci. We provide the matrices for L up to 4 and also include a computer program to automatically generate the matrices for higher values of L. Furthermore, our framework can be generalized to recombination rates that are different in female and male meiosis which allows us to show that the Haldane and Waddington 2-locus formula is valid in that more subtle case if the meiotic recombination rate is taken as the average rate across female and male. Once the 4L IBD probabilities are determined, the 2L probabilities of RIL genotypes are obtained via summations of these quantities. In fine, our computer program allows to determine the probabilities of all the multilocus genotypes produced in such sibling-based RILs for L ≤ 10, a huge leap beyond the L = 3 restriction of Haldane and Waddington.

First evidence of asexual recruitment of Pocillopora acuta in Okinawa Island using genotypic identification

Okinawa Island is located near the center of the Nansei Islands (∼24–31°N), at a relatively high latitude for coral reefs. Nevertheless, more than 80 coral genera (over 400 species) are abundant in the Nansei Islands. Since March, 2017, scleractinian corals have been held in an outdoor tank at the OIST Marine Science Station at Seragaki, Onna with natural sea water flow-through in order to be used in molecular biological and physiological studies. In January, 2018, we found small pocilloporid-like colonies suspected to have originated asexually. We collected 25 small colonies and measured their sizes and weights. Also, we validated the classification and clonality of the colonies using a mitochondrial locus and nine microsatellite loci. Almost all of the small colonies collected in the outdoor tank were ≤1 cm in both width and height. The weight of dried skeletons ranged from 0.0287 to 0.1807 g. Genetic analysis determined that they were, in fact, Pocillopora acuta. Only one mitochondrial haplotype was shared and two microsatellite multilocus genotypes were detected (20 colonies of one and four colonies of the other). The mitochondrial haplotype and one microsatellite multilocus genotype for 20 colonies corresponded to those of one P. acuta colony being kept in the tank. One small colony matched both multilocus genotypes. This may have been a chimeric colony resulting from allogenic fusion. These small colonies were not produced sexually, because the only potential parent in the tank was the aforementioned P. acuta colony. Instead, they were more likely derived from asexual planula release or polyp bail-out. Corals as Pocillopora acuta have the capacity to produce clonal offspring rapidly and to adapt readily to local environments. This is the first report of asexual reproduction by planulae or expelled polyps in P. acuta at Okinawa Island.