Use of the HLA-B leader to optimize cord-blood transplantation

Cord-blood transplantation (CBT) can cure life-threatening blood disorders. The HLA-B leader affects the success of unrelated donor transplantation but its role in CBT is unknown. We tested the hypothesis that the HLA-B leader influences CBT outcomes in unrelated single-unit cord-blood transplants performed by Eurocord/European Blood and Marrow Transplant (EBMT) centers between 1990 and 2018 with data reported to Eurocord. Among 4822 transplants, 2178 had one HLA-B mismatch of which 1013 were HLA-A and HLA-DRB1-matched. The leader (M or T) was determined for each HLA-B allele in patients and units to define the genotype. Among single HLA-B-mismatched transplants, the patient/unit mismatched alleles were defined as leader-matched if they encoded the same leader, or leader-mismatched if they encoded different leaders; the leader encoded by the matched (shared) allele was determined. The risks of GVHD, relapse, non-relapse mortality and overall mortality were estimated for various leaderdefined groups using multivariable regression models. Among the 1013 HLA-A, -DRB1- matched transplants with one HLA-B mismatch, increasing numbers of cord-blood unit M-leader alleles was associated with increased risk of relapse (hazard ratio [HR] for each increase in one M-leader allele 1.30, 95% confidence interval [CI] 1.05 to 1.60, P 0.02). Furthermore, leader mismatching together with an M-leader of the shared HLA-B allele lowered non-relapse mortality (HR 0.44, 95% CI 0.23 to 0.81; P 0.009) relative to leader-matching and a shared T-leader allele. The HLA-B leader may inform relapse and non-relapse mortality risk after CBT. Future patients might benefit from the appropriate selection of units that consider the leader.

Studi Kekerabatan Padi Hasil Piramidisasi Berbasis Marka Molekuler dan Fenotipik

Piramidisasi gen adalah upaya untuk menggabungkan beberapa gen yang menguntungkan dari banyak tetua menjadi satu genotipe tunggal. Hasil tinggi, tahan terhadap wereng cokelat, kandungan amilosa sedang, umur genjah dan aromatik adalah beberapa sifat yang diharapkan untuk digabungkan. Melalui teknik piramidsasi, telah diperoleh 28 genotip, namun analisis kekerabatan genetik, sebagai pertimbangan dalam pengambilan keputusan pada tahapan pemuliaan selanjutnya, belum dilakukan. Kombinasi gen ini dicapai dengan persilangan banyak genotipe tetua dengan karakter unggul yaitu Sintanur (aromatik), Pandan Wangi (aromatik), IR64 (kandungan amilosa sedang), PTB33 (tahan wereng coklat), Ciapus (hasil tinggi) dan KA (umur genjah). Tujuan percobaan ini adalah untuk memperoleh hubungan genetik genotip dalam sifat-sifat agro-morfologi dan marka molekuler. Analisis hubungan kekerabatan antara tetua dan 28 genotip piramidisasi dilakukan menggunakan software XLSTAT2016 untuk membentuk matrik similarity shared allele distance dengan koefisien Jaccard sebagai pembentuk jarak genetik untuk marka molekuler dan koefisien korelasi pearson untuk marka fenotipik. Kemudian dilakukan pengelompokan atau clustering dengan metode Unweighted Pair Group Method with Arithmetic Averages (UPGMA). Hasil pengelompokan berdasarkan marka molekuler dengan menggunakan 11 marka yang terkait erat dengan tujuh karakter target, diperoleh koefisien kemiripan sebesar 41,3% dan terbentuk dua kelompok, sedangkan hasil pengelompokan berdasarkan marka fenotipik dengan 14 karakter agro-morfologi terbentuk tiga kelompok dengan tingkat kemiripan 22,2%. Genotipe SPxCAKA1B, SPxPP3B dan PPxIP4B dapat dimanfaatkan sebagai tetua atau genotipe harapan karena memiliki jarak kekerabatan yang paling jauh diantara genotip lainnya.

EVALUACIÓN DE LA VARIABILIDAD GENÉTICA DE SHIHUAHUACO Dipteryx ferrea (Ducke) Ducke EN LA AMAZONÍA PERUANA, MEDIANTE MARCADORES MICROSATÉLITES

Se evaluó la variabilidad genética del shihuahuaco, Dipteryx ferrea, en siete poblaciones naturales en la Amazonía peruana mediante el análisis de nueve loci microsatélites. Los resultados muestran una alta diversidad genética evidenciada en el elevado polimorfismo (total alelos = 135, media de alelos por locus = 15 ± 6 alelos) y riqueza alélica (Macuya = 11 e Iñapari = 8, máxima y mínima riqueza alélica, respectivamente). El análisis de componentes principales muestra una fuerte superposición entre las poblaciones, que sumado a los reducidos valores de distancia genética interpoblacional (valores entre 0.07 a 0.10), revela una elevada semejanza genética entre las poblaciones. El dendrograma elaborado en base a la distancia genética de Shared Allele, muestra que las poblaciones se encuentran conformando tres agrupaciones genéticas principales, la primera constituida por Manu e Iñapari (grupo A, bootstrap = 91%), la segunda por Contamana y Macuya (grupo B, 60%), y la tercera por Tamaya, Santa Clara e Inuya (grupo C, 100%). El análisis de correlación mostró que existe una correlación positiva entre la distancia geográfica y distancia genética entre las poblaciones analizadas (r = 0.62, p < 0.005). La elevada similitud genética entre poblaciones encontrada en esta especie puede ser atribuida al sistema de reproducción alógama (polinización cruzada) que presenta el shihuahuaco, a sus polinizadores (murciélagos, abejas) y dispersores (guacamayos, águilas, pecaríes, etc.) que pueden desplazarse grandes distancias geográficas facilitando el flujo de genes entre las poblaciones. Factores históricos como la actividad tectónica de la zona de estudio también influyeron en las relaciones genéticas observadas entre las poblaciones, distinguiendo grupos genéticos hermanos como A y B que cubren gran parte de la distribución geográfica de la especie y un grupo diferenciado (grupo C) ubicado en una zona de formación más reciente en el departamento de Ucayali.

Short-read DNA Sequencing Yields Microsatellite Markers for Rheum

Identifying and evaluating genetic diversity of culinary rhubarb (Rheum ×rhababarum) cultivars using morphological characteristics is challenging given the existence of synonyms and nomenclatural inconsistencies. Some cultivars with similar names are morphologically different, and seedlings may grow and become associated with the parental name. Morphological traits of one cultivar may vary when measured under different environmental conditions. Molecular markers are consistent for unique genotypes across environments and provide genetic fingerprints to assist in resolving identity issues. Microsatellite repeats, also called simple sequence repeats (SSRs), are commonly used for fingerprinting fruit and nut crops, but only 10 SSRs have previously been reported in rhubarb. The objectives of this study were to use short-read DNA sequences to develop new di-nucleotide-containing SSR markers for rhubarb and to determine if the markers were useful for cultivar identification. A total of 97 new SSR primer pairs were designed from the short-read DNA sequences. The amplification success rate of these SSRs was 77%, whereas polymorphism of those reached 76% in a test panel of four or eight rhubarb individuals. From the 57 potentially polymorphic primer pairs obtained, 25 SSRs were evaluated in 58 Rheum accessions preserved in the U.S. Department of Agriculture, National Plant Germplasm System. The primer pairs generated 314 fragments with an average of 12.6 fragments per pair. The clustering of many accessions in well-supported groups supported previous findings based on amplified fragment length polymorphisms (AFLPs). Cluster analysis, using the proportion of shared allele distance among the 25 SSRs, distinguished each of the 58 accessions including individuals that had similar names or the same name. Accessions that grouped in well-supported clusters previously belonged to similar clusters with high bootstrap support based on AFLP. In summary, our technique of mining short-read sequencing data was successful in identifying 97 di-nucleotide-containing SSR sequences. Of those tested, the 25 most polymorphic and easy-to-score primer pairs proved useful in fingerprinting rhubarb cultivars. We recommend the use of short-read sequencing for the development of SSR markers in the identification of horticultural crops.

Molecular characterization of barley (Hordeum vulgare L.) accessions of the Serbian GeneBank by SSR fingerprinting

Molecular diversity of 145 barley (Hordeum vulgare subsp. vulgare L.) accessions from the Serbian GenBank was assessed by single sequence repeats (SSR) markers. A set of 15 SSRs, covering all chromosomes of the diploid barley genome with 2-3 SSR markers per chromosome, with a range of 4-18 alleles per locus were used. In total, 15 loci and 119 alleles were detected, with an average of 7.93 alleles per locus. The Polymorphic information content value ranged from 0.220 to 0.782 with a mean value of 0.534. Regarding the growth habit and row type groups, gene diversity was comparatively higher for the spring (0.616) and six-rowed accessions (0.616) than for the winter and two- rowed accessions (0.322 and 0.478, respectively). Analysis of molecular variance showed that all sources of variation were significant (P < 0.01), but the between-group component was predominant (76.85%) for growth habit and 89.45% for row type. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on the shared allele distance (DSA) matrix estimated on the SSR data assigned the genotypes into two clusters - the first smaller consisting of the six 6-rowed spring cultivars and the second comprising six subclusters. Genotype MBR1012 was separated from all other genotypes that constitute UPGMA tree. The associations of genotypes belonging to different growth habit and row type groups were assessed using Principal Coordinate Analysis revealing separation of winter growth habit group from facultative one. The use of the STRUCTURE clustering algorithm allowed the identification of 2 subpopulations of genotypes.

Coevolutionary fine-tuning: evidence for genetic tracking between a specialist wasp parasitoid and its aphid host in a dual metapopulation interaction

In the interaction between two ecologically-associated species, the population structure of one species may affect the population structure of the other. Here, we examine the population structures of the aphidMetopeurum fuscoviride, a specialist on tansyTanacetum vulgare, and its specialist primary hymenopterous parasitoidLysiphlebus hirticornis, both of which are characterized by multivoltine life histories and a classic metapopulation structure. Samples of the aphid host and the parasitoid were collected from eight sites in and around Jena, Germany, where both insect species co-occur, and then were genotyped using suites of polymorphic microsatellite markers. The host aphid was greatly differentiated in terms of its spatial population genetic patterning, while the parasitoid was, in comparison, only moderately differentiated. There was a positive Mantel test correlation between pairwise shared allele distance (DAS) of the host and parasitoid, i.e. if host subpopulation samples were more similar between two particular sites, so were the parasitoid subpopulation samples. We argue that while the differences in the levels of genetic differentiation are due to the differences in the biology of the species, the correlations between host and parasitoid are indicative of dependence of the parasitoid population structure on that of its aphid host. The parasitoid is genetically tracking behind the aphid host, as can be expected in a classic metapopulation structure where host persistence depends on a delay between host and parasitoid colonization of the patch. The results may also have relevance to the Red Queen hypothesis, whereupon in the ‘arms race’ between parasitoid and its host, the latter ‘attempts’ to evolve away from the former.

Characterization of Simple Sequence Repeat (SSR) Markers and Genetic Relationships within Cultivated Peanut (Arachis hypogaea L.)

A total of 709 SSR markers were collected from public databases and 556 SSRs passed an initial screen and were used to characterize 16 peanut (Arachis hypogaea) genotypes. PIC (polymorphism information content) scores and heterozygosity indices for each marker were calculated to assess the genetic diversity revealed by SSR markers and genetic distances were estimated from shared allele distances for construction of a cladogram by the Neighbor-Joining method to illustrate the genetic relationships among the genotypes. Two hundred thirty-five (42.27%) markers showed polymorphisms in these genotypes. The average heterozygosity estimated from these 556 SSRs was 0.225 with a range of 0 to 0.992 and the average PIC was 0.209. The average number of alleles per SSR was 2.5 with a range of 1 to 13. However, 410 SSR markers had only one allele, confirming that diversity of cultivated peanuts is very limited. Among the polymorphic SSR markers, 26.4% were dinucleotide GA repeat motif markers, followed by dinucleotide CT (10.4%), and trinucleotide TAA (9.6%). The dinucleotide and trinucleotide repeat motifs are the most abundant type of SSRs, and dinucleotide GA repeat motif shows a higher polymorphism in comparison to other types. The genetic relationships revealed from the cladogram are in agreement with the pedigrees and origins of the tested peanut genotypes, indicating that these SSR markers are useful tools for evaluation of genetic diversity in peanuts.

Rejection patterns in botryllid ascidian immunity: the first tier of allorecognition

Botryllid ascidians, a small but geographically widely distributed group of compound tunicates, are being used as a model system for the study of allorecognition. Botryllid ascidians possess a unique type of immunity. Pairs of colonies that meet through their extending ampullae either fuse to form a chimera or develop cytotoxic lesions at contact zones (rejection). This first tier of allorecognition is succeeded (in cases of fusion) by two additional tiers, not reviewed here (the colony resorption phenomenon and the phenomenon of somatic and germ cell parasitism). Fusion and rejection are controlled by a single highly polymorphic gene locus termed the fusibility/histocompatibility (Fu/HC) locus. One shared allele on the Fu/HC locus is enough for fusion. Rejecting colonies do not share any Fu/HC alleles. To date, 14 botryllid ascidians have been studied for their fusibility patterns; of these, the cosmopolitan species Botryllus schlosseri (Pallas, 1766) has emerged as the most studied taxon. This review summarizes studies revealing the various types of noncompatible responses that are expressed following the application of the "colony allorecognition assay" and the "cut surface assay". These include divergent alloresponses related to different populations of the same botryllid species, distinctive allorecognition sites, polymorphism and a repertoire of Fu/HC alleles, a state of low responsiveness as opposed to the expected immunological memory, the retreat growth phenomenon, and the irreversible nature of the rejection process. A detailed description of the accumulated knowledge on the effector cells (morula cells and macrophages), the humoral and cellular molecules (at the biochemical and molecular levels), and the prophenoloxidase system is given. Links between allogeneic responses and the evolutionary ecology of botryllid ascidians are revealed. Since tunicates occupy a key phylogenetic position in the origin of the vertebrates, the study of colony allorecognition in this group may shed light on self/nonself recognition elements in other multicellular organisms, including vertebrates.

Inferring Modes of Colonization for Pest Species Using Heterozygosity Comparisons and a Shared-Allele Test

Long-range dispersal of a species may involve either a single long-distance movement from a core population or spreading via unobserved intermediate populations. Where the new populations originate as small propagules, genetic drift may be extreme and gene frequency or assignment methods may not prove useful in determining the relation between the core population and outbreak samples. We describe computationally simple resampling methods for use in this situation to distinguish between the different modes of dispersal. First, estimates of heterozygosity can be used to test for direct sampling from the core population and to estimate the effective size of intermediate populations. Second, a test of sharing of alleles, particularly rare alleles, can show whether outbreaks are related to each other rather than arriving as independent samples from the core population. The shared-allele statistic also serves as a genetic distance measure that is appropriate for small samples. These methods were applied to data on a fruit fly pest species, Bactrocera tryoni, which is quarantined from some horticultural areas in Australia. We concluded that the outbreaks in the quarantine zone came from a heterogeneous set of genetically differentiated populations, possibly ones that overwinter in the vicinity of the quarantine zone.

Transmission Genetics of Allorecognition in Hydractinia symbiolmgicarpus (Cnidaria: Hydrozoa)

Allorecognition is ubiquitous, or nearly so, amongst colonial invertebrates. Despite the prominent role that such phenomena have played both in evolutionary theory and in speculations on the origin of the vertebrate immune system, unambiguous data on the transmission genetics of fusibility (i.e., the ability of two individuals to fuse upon tissue contact) is lacking for any metazoan outside of the phylum Chordata. We have developed lines of the hydroid Hydractinia symbiolongzcarpus (Phylum Cnidaria) inbred for fusibility and here report results of breeding experiments establishing that fusibility segregates as expected for a single locus with codominantly expressed alleles, with one shared allele producing a fusible phenotype. Surveys of fusibility in field populations and additional breeding experiments indicate the presence of an extensive allele series.