Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law

Alternative splicing is ubiquitous, but the mechanisms underlying its pattern of evolutionary divergence across mammalian tissues are still underexplored. Here, we investigated the cis-regulatory divergences and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid between two mouse species. Large splicing changes between tissues are highly conserved and likely reflect functional tissue-dependent regulation. In particular, micro-exons frequently exhibit this pattern with high inclusion levels in the brain. Cis-divergence of splicing appears to be largely non-adaptive. Although divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform apparently tolerate more mutations, explaining why their exon sequences are highly conserved but their intronic splicing site flanking regions are not. Moreover, we demonstrate that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attribute such buffering effect to trans-regulatory splicing efficiency.

Hybrids of Solanum corymbiflorum and S. diploconos (Solanaceae) – a hope for new commercial varieties of edible fruits

Solanum diploconos (Mart.) Bohs („guava tamarillo”) and Solanum corymbiflorum (Sendtn.) Bohs („hardy tamarillo”) are wild relatives to subtropical, orchard, small tree – Solanum betaceum Cav. (called simply „tamarillo”). Both these species create edible fruits, but they have not been cultivated widely so far as fruit trees. However, each one of these species has valuable features. Solanum corymbiflorum is quite hardy to frost, deciduous and early blooming both in fenological year time as well as in its lifespan but has untasty fruits. Solanum diploconos has quite good tasting fruits and it is pest and disease resistant. This work has been an attempt to connect their best features in hybrids to create new, potentially commercial cultivars to grow as fruit plants. Three types of hybrids were created: F1 hybrid type – Solanum corymbiflorum × Solanum diploconos, BC1 backrossing type - (Solanum corymbiflorum × Solanum diploconos) × Solanum corymbiflorum and the second BC1 backcrossing type – (Solanum corymbiflorum × Solanum diploconos) × Solanum diploconos. Out of the numerous variable individuals within each type, we selected three very valuable from an agronomic point of view cultivars (Solanum 'Lynn', 'Pinczow Springs' and 'Iwona'). The work with crossing and selecting the next cultivars will be continued.

Characterization of sequence determinants of enhancer function using natural genetic variation

Sequence variation in enhancers, a class of cis-regulatory elements that control cell type-specific gene transcription, contributes significantly to phenotypic variation within human populations. Enhancers are short DNA sequences (~200 bp) composed of multiple binding sites (4-10 bp) for transcription factors (TFs). The transcriptional regulatory activity of an enhancer is encoded by the type, number, and distribution of TF binding sites that it contains. However, the sequence determinants of TF binding to enhancers and the relationship between TF binding and enhancer activity are complex, and thus it remains difficult to predict the effect of any given sequence variant on enhancer function. Here, we generate allele-specific maps of TF binding and enhancer activity in fibroblasts from a panel of F1 hybrid mice that have a high frequency of sequence variants. We identified thousands of enhancers that exhibit differences in TF binding and/or activity between alleles and use these data to define features of sequence variants that are most likely to impact enhancer function. Our data demonstrate a critical role for AP-1 TFs at many fibroblast enhancers, reveal a hierarchical relationship between AP-1 and TEAD TF binding at enhancers, and delineate the nature of sequence variants that contribute to AP-1 TF binding. These data represent one of the most comprehensive assessments to date of the impact of sequence variation on enhancer function in chromatin, with implications for identifying functional cis-regulatory variation in human populations.

Quantitative Trait Loci and Candidate Genes Associated with Cold-Acclimation and Microdochium nivale Tolerance/Susceptibility in Winter Triticale (x Triticosecale)

Tolerance to pink snow mold caused by Microdochium nivale appears after a cold-hardening period and it is an essential, genotype-dependent, complex quantitative trait for the wintering of triticale (x Triticosecale) and other cereals. Despite long-term studies, a marker for the selection of the tolerant genotypes is still insufficiently recognized. Chlorophyll fluorescence has been reported as a sensitive indicator of stress effects on photosynthesis and can be used to predict plant tolerance. In this study, the genomic regions (QTLs) associated with the level of winter triticale seedlings damage caused by M. nivale infection as well as photosynthesis quantum efficiency and chlorophyll a fluorescence parameters were identified in seedlings of mapping population of 89 doubled haploids lines (DHs) derived from F1 hybrid of cv. ‘Hewo’ and cv. ‘Magnat’ accompanied with the genetic map consisting of 20 linkage groups with a total map length 4997.4 cm. Independent experiments performed in controlled conditions revealed 13 regions identified by a composite interval mapping, located on 7A, 1B, 2B, 6B, 7B, 3R, 5R, and 6R linkage groups and related to the PI, PIABS, TRo/CS, ABS/CS, ABS/CSm, ABS/RC, and Qy values as well as M. nivale tolerance T and susceptibility level P expressed by the seedling damage index. Additionally, candidate genes were in silico identified with the sequence position on wheat (2B and 7B) and rye (5R) chromosomes, where relevant QTL regions were found. The most important candidate genes indicated for M. nivale tolerance of cold-hardened triticale seedlings include those coding: sterol 3-beta-glucosyltransferase UGT80A2-like, transcription factor NAI1-like, and flavonol3-sulfotransferase-like proteins on chromosomes 2B and 5R.

Susceptibility Assessment of Two Tomato Hybrids Against Tuta absoluta Infestation Under Greenhouse Conditions

Abdel-Razek, A.S., N.M. Abd El-Ghany, M.A. Gesraha, T.A. Elewa and A. Moussa. 2021. Susceptibility Assessment of Two Tomato Hybrids Against Tuta absoluta Infestation Under Greenhouse Conditions. Arab Journal of Plant Protection, 39(4): 317-322. https://doi.org/10.22268/AJPP-39.4.317322 Tuta absoluta is a major insect pest which attack tomato plant varieties in Egypt. Several control attempts were carried out to avoid major crop losses by heavy application of chemical insecticides. The aim of the present study is to assess the susceptibility of infestation of T. absoluta of two tomato varieties (Shifa and Savera F1 hybrids) under greenhouse conditions. The tomato varieties were planted in two plantation periods at the district of Kom Hamada, El-Nubaria province, El-Behira Governorate. The susceptibility tests were done by random counting of leaf samples for the presence of T. absoluta mines and larvae. Both tomato varieties showed almost the same T. absoluta infestation level. Moreover, yield assessment was carried out for the two plantation periods by taking the average fruit weight yield (Kg/acre). The tomato yield results showed that Savera F1 hybrid tomato had higher yield compared to Shifa F1 hybrid variety, but such difference was not significant, However, the yield difference of both vireties between the two planting dates was significant. Keywords: Tomato, Tuta absoluta, susceptibility, leaf-mine, larvae, yield.

Organelle genome assembly uncovers the dynamic genome reorganization and cytoplasmic male sterility associated genes in tomato

To identify cytoplasmic male sterility (CMS)-associated genes in tomato, we determined the genome sequences of mitochondria and chloroplasts in three CMS tomato lines derived from independent asymmetric cell fusions, their nuclear and cytoplasmic donors, and male fertile weedy cultivated tomato and wild relatives. The structures of the CMS mitochondrial genomes were highly divergent from those of the nuclear and cytoplasmic donors, and genes of the donors were mixed up in these genomes. On the other hand, the structures of CMS chloroplast genomes were moderately conserved across the donors, but CMS chloroplast genes were unexpectedly likely derived from the nuclear donors. Comparative analysis of the structures and contents of organelle genes and transcriptome analysis identified three genes that were uniquely present in the CMS lines, but not in the donor or fertile lines. RNA-sequencing analysis indicated that these three genes transcriptionally expressed in anther, and identified different RNA editing levels in one gene, orf265, that was partially similar to ATP synthase subunit 8, between fertile and sterile lines. The orf265 was a highly potential candidate for CMS-associated gene. This study suggests that organelle reorganization mechanisms after cell fusion events differ between mitochondria and chloroplasts, and provides insight into the development of new F1 hybrid breeding programs employing the CMS system in tomato.

Evaluation of onion samples (Allium cepa L.) of various origins in the foothill zone of the North Caucasus and creation of source material fo

Relevance. The success of breeding work is largely determined by the source material, the search and creation of which for target breeding begins with the collection and study of collectible samples for the alignment of morphological features; for the precocity and amity of maturation; for the keeping quality and transportability of bulbs; for the quality of vegetable products (high content of biologically active substances and antioxidants); for resistance to biotic and abiotic stressors of a specific growing zone.Materials and methods. On the basis of the North Caucasus branch FSBSI FSVC, 90 samples of spring onions from 26 countries of the world were evaluated in the number nursery for the period from 2017 to 2019, 71 of them were varieties and 19 were F1 hybrids. In a hybrid nursery, 25 hybrid combinations obtained from FSBSI FSVC (VNIISSOK) were evaluated. The laying and placement of experiments, agricultural techniques of cultivation, accounting and evaluation of economically valuable traits, biochemical analyses were carried out according to generally accepted methods. The standards are the new Primo and Ampex varieties of the selection of the FSBSI FSVC and the Italian F1 hybrid Ranko, which were placed every 10 collection samples.Results.According to the results of the assessment, among the studied F1 varieties and hybrids, sources of economically valuable traits such as yield (20-27 t/ha), precocity (80-90 days), preservation (more than 85%) when laid for long-term storage up to 7 months, purple, white and pink color of bulbs, as well as sources of long-shaped bulbs were identified. The greatest interest for breeding for yield is represented by 9 promising varieties and 9 F1 hybrids of onions of various origins, as well as 4 hybrid combinations that were distinguished by high yields, the yield of marketable products and the mass of marketable bulbs. These samples are recommended for use in the breeding process as sources for the creation of new varieties and hybrids with high yields for the agro-climatic conditions of the foothill zone of the North Caucasus.r breeding

Identity of genes of resistance to broomrape race G in sunflower lines of different origin

Broomrape is an obligate parasite and one of the most significant biotic factors reducing sunflower yield. The main means of controlling broomrape is breeding for sunflower resistance to it. New strategies are required to develop parasite resistant breeding germplasm, such as a stacking of key genes or a combination of qualitative and quantitative resistance mechanisms. In this regard, it is necessary to keep searching for new sources of resistance and to combine existing genes in case they are not identical. Thus, it is necessary to determine whether the genes of resistance to race G of broomrape are identical in the sunflower lines bred at the V.S. Pustovoit All-Russian Research Institute of Oil Crops. The research material was the previously developed sunflower lines RG, RGP1, RGP2, RGВ, RGL1, RGL2, and RGM – donors of resistance to race G of broomrape. The F1 hybrids from pair crossbreeding of these lines were obtained in a greenhouse. The F2 hybrids were obtained in the field by self-pollination of F1 hybrid plants. Plants were tested in a greenhouse for resistance and susceptibility to broomrape using the method of early diagnosis. Mathematical processing was performed by using the χ 2 -test. 13 combinations of crossbreeding were received to complete the test for allelism. In each F1 combination 11–33 plants were evaluated for resistance to race G of broomrape. Among the tested combinations, there was no one resistant to broomrape. Despite the differences in the number of affected plants, the affection degree was small in all hybrid combinations – from 1.0 to 1.8. All F2 hybrid combinations were also affected by broomrape. For eight combinations of F2, two phenotypic classes were found. There was no segregation in three combinations. The number of plants of two combinations was too small to perform χ 2 -test. In general, the χ 2 values were higher than the acceptable ones with a probability of 0.05, which indicates that the genes of resistance to race G of broomrape in these lines are identical.

PROGRESSES ON THE NATURE AND BIOTIC STRESS OF POTATO (SOLANUM TUBEROSUM L.)

Potato (Solanum tuberosum L.) is the third largest crop in terms of consumption by human, most important tuber crop in the world and a vital plant for global food security. Instead, potato breeding is slow compared to other crops. Transforming potato into a diploid F1 hybrid crop is a hopeful method to increase potato genetic gain. Studies on breeding and genetics of potato has big potential to solve many problems exist in potato. Another potential area for these studies are diseases which are seriously targeting this crop worlwide started from Irish potato famine which effected whole Europe continent. Here in this review, some of latest significant problems and approaches related to potato production are given below.

Physiological and Agronomic Traits of Certain Sugarcane Genotypes Grown under Field Conditions as Influenced by Early Drought Stress

Drought is one of the important problems that drastically affect sugarcane production in several countries. The objective of this research was to investigate the effects of early drought stress on physiological parameters and agronomic traits of six sugarcane genotypes under field conditions. The experiment was arranged in a split plot in a completely randomized block design with three replications. The main plot was represented by three different water regimes: field capacity (FC), ½FC and rain-fed (RF) whereas, the subplot consisted of six sugarcane genotypes: KK3 (drought tolerant), Q117 (drought tolerant), LK92-11 (drought susceptible), Ths98-271 (S. spontaneum), KK08-214 (the F1 hybrid derived from S. spontaneum × S. officinarum) and E08-4-019 (the F1 hybrid derived from Erianthus sp. × S. officinarum). The six sugarcane genotypes were subjected to three irrigation treatments. The 45-day-old plants of all sugarcane genotypes were exposed to drought by withholding water for 72 days. Certain photosynthetic parameters were measured in the leaves of four-month-old plants. Certain cane yield parameters were measured in the 12-month-old plants. The results showed that early drought stress decreased the maximum quantum yield of PSII efficiency, net photosynthetic rate, transpiration rate and stomatal conductance. Drought stress significantly (p ≤ 0.01) decreased cane yield. The cane yield and sugar yield of KK3 were significantly (p ≤ 0.01) higher than those of the other genotypes. The wild-type sugarcane and the F1 hybrids derived from the wild and commercial sugarcane could maintain better photosynthetic performance while encountering early drought stress.