Introgression Of Genes Research Articles

Phylogenomics of Paragymnopteris (Cheilanthoideae, Pteridaceae): Insights from plastome, mitochondrial, and nuclear datasets

Previous studies have shown that at least six genera of the Cheilanthoideae, a subfamily of the fern family Pteridaceae, may not be monophyletic. In these non-monophyletic genera, the Old-World genus Paragymnopteris including approximately five species have long been controversial. In this study, with an extensive taxon sampling of Paragymnopteris, we assembled 19 complete plastomes of all recognized Paragymnopteris species, plastomes of Pellaea (3 species) and Argyrochosma (1 species), as well as transcriptomes from Paragymnopteris (6 species) and Argyrochosma (1 species). We conducted a comprehensive and systematic phylogenomic analysis focusing on the contentious relationships among the genus of Paragymnopteris through 9 plastid makers, the plastomes, mitochondria, nuclear ribosomal cistron genomes, and single-copy nuclear genes. Moreover, we further combined distribution, ploidy, and morphological features to investigate the evolution of Paragymnopteris. The backbone of Paragymnopteris was resolved consistently in the nuclear and plastid phylogenies. Our major results include: (1) Paragymnopteris is not monophyletic including two fully supported clades; (2) confirming that Paragymnopteris delavayi var. intermedia is a close relative of P. delavayi instead of P. marantae var. marantae; (3) the chromosome base number may not be a stable trait which has previously been used as an important character to divide Paragymnopteris into two groups; and (4) gene flow or introgression might be the main reason for the gene trees conflict of Paragymnopteris, but both gene flow and ILS might simultaneously and/or cumulatively act on the conflict of core pellaeids. The robust phylogeny of Paragymnopteris presented here will help us for the future studies of the arid to semi-arid ferns of Cheilanthoideae at the evolutionary, physiological, developmental, and omics-based levels.

Multi-Approach Unveils Potential Gene Introgression of Oil Camellias

The complex phylogenetic relationship of polyploid species provides an opportunity for a comprehensive study of gene introgression. Oil camellias refer to a class of important woody oil plant in the camellia genus, including octoploid, hexaploid, tetraploid, and diploid plants, but the phylogeny relationship of these species remains poorly investigated. Here, based on multiple types of evidence, including phylogenetic conflict, gene flow analysis, and representative metabolite, we reconstructed the phylogenetic relationship of oil camellias. Camellia shensiensis and C. grijsii formed a distinct branch. Phylogenetic conflict suggested that hexaploid C. oleifera probably originated from hybridization and clustered with diploid C. kissi and tetraploid C. meiocarpa. Tetraploid C. confusa probably originated from crossing the ancestor of C. kissi and C. brevistyla, and C. brevistyla probably was the maternal progenitor of hexaploid C. sasanqua. Furthermore, the composition of anthocyanin in tender leaves showed a strong correlation with phylogenetic distinctions. This study proves the feasibility of using iconic metabolic components to solve phylogenetic relationships and lays a foundation for analyzing genetic breeding and utilizing oil camellia resources.

Sequential introgression of a carotenoid processing gene underlies sexual ornament diversity in a genus of manakins.

In a hybrid zone between two tropical lekking birds, yellow male plumage of one species has introgressed asymmetrically replacing white plumage of another via sexual selection. Here, we present a detailed analysis of the plumage trait to uncover its physical and genetic bases and trace its evolutionary history. We determine that the carotenoid lutein underlies the yellow phenotype and describe microstructural feather features likely to enhance color appearance. These same features reduce predicted water shedding capacity of feathers, a potential liability in the tropics. Through genome-scale DNA sequencing of hybrids and each species in the genus, we identify BCO2 as the major gene responsible for the color polymorphism. The BCO2 gene tree and genome-wide allele frequency patterns suggest that carotenoid-pigmented collars initially arose in a third species and reached the hybrid zone through historical gene flow. Complex interplay between sexual selection and hybridization has thus shaped phenotypes of these species, where conspicuous sexual traits are key to male reproductive success.

Microsatellite Markers & Mitochondrial D-Loop Based Phylogenetic And Diversity Analysis In Gabrali Cattle.

The Gabrali cattle is a multipurpose breed, native to Khyber Pakhtunkhwa, Pakistan. Despite its economic importance, scientific data about its phylogeny and genetic diversity is scarce. To address this issue, the present study was conducted on thirty (30) unrelated Gabrali male and female animals, from which blood samples were collected and DNA was extracted. Twelve (12) microsatellite loci and 1159bp of D-loop region were amplified via PCR and visualized on a 2% agarose gel. Sanger sequencing technique was used to sequence the D-loop amplicons. The microsatellite loci revealed 83 alleles with MNA (mean no of alleles per locus) = 8.8, the Ho (observed heterozygosity) and He (expected heterozygosity) of all loci were 0.58 and 0.50 respectively, mean PIC (Polymorphic Information content) = 0.59 and FIS (Inbreeding coefficient) = 0.056 using GeneAlEx® software. Microsatellite analysis revealed a normal allelic distribution across the breed, consistent with Hardy-Weinberg equilibrium. D-loop sequencing revealed eight haplotypes with 30 SNPs using DNA SP 6.0 software. High AT content was observed than GC content i.e. 55.9% and 44.1% respectively, while the transition to transversion ratio was R = 10:1. The value of Haplotype and Nucleotides diversity was Hd = 0.8601 ± SD = 0.0895 and Π = 0.0136 ± SD = 0.00197 respectively. Phylogenetic analysis done using Neighbor-joining method with bootstraps value of 1000, revealed the monophyletic clade of both Gabrali and Bos indicus haplotypes. Furthermore, the introgression of genes from national cattle breeds into Gabrali cattle was observed. It is concluded that Gabrali cattle have common ancestry with Bos indicus having no threats of genetic bottleneck having substantial genetic diversity.

Pangenome Data Analysis Reveals Characteristics of Resistance Gene Analogs Associated with Sclerotinia sclerotiorum Resistance in Sunflower

The sunflower, an important oilseed crop and food source across the world, is susceptible to several pathogens, which cause severe losses in sunflower production. The utilization of genetic resistance is the most economical, effective measure to prevent infectious diseases. Based on the sunflower pangenome, in this study, we explored the variability of resistance gene analogs (RGAs) within the species. According to a comparative analysis of RGA candidates in the sunflower pangenome using the RGAugury pipeline, a total of 1344 RGAs were identified, comprising 1107 conserved, 199 varied, and 38 rare RGAs. We also identified RGAs associated with resistance against Sclerotinia sclerotiorum (S. sclerotiorum) in sunflower at the quantitative trait locus (QTL). A total of 61 RGAs were found to be located at four quantitative trait loci (QTLs). Through a detailed expression analysis of RGAs in one susceptible and two tolerant sunflower inbred lines (ILs) across various time points post inoculation, we discovered that 348 RGAs exhibited differential expression in response to Sclerotinia head rot (SHR), with 17 of these differentially expressed RGAs being situated within the QTL regions. In addition, 15 RGA candidates had gene introgression. Our data provide a better understanding of RGAs, which facilitate genomics-based improvements in disease resistance in sunflower.

Introgression of Herbicide-Resistant Gene from Genetically Modified Brassica napus L. to Brassica rapa through Backcrossing.

Interspecific hybridization between two different Brassicaceae species, namely Brassica rapa ssp. pekinensis (♀) (AA, 2n = 2x = 20) and genetically modified Brassica napus (♂) (AACC, 2n = 4x = 38), was performed to study the transmission of a herbicide resistance gene from a tetraploid to a diploid Brassica species. Initially, four different GM B. napus lines were used for hybridization with B. rapa via hand pollination. Among the F1 hybrids, the cross involving the B. rapa (♀) × GM B. napus (♂) TG#39 line exhibited the highest recorded crossability index of 14.7 ± 5.7. However, subsequent backcross progenies (BC1, BC2, and BC3) displayed notably lower crossability indices. The F1 plants displayed morphological characteristics more aligned with the male parent B. napus, with significant segregation observed in the BC1 generation upon backcrossing with the recurrent parent B. rapa. By the BC2 and BC3 generations, the progeny stabilized, manifesting traits from both parents to varying degrees. Cytogenetic analysis revealed a substantial reduction in chromosome numbers, particularly in backcrossing progenies. BC1 plants typically exhibited 21-25 chromosomes, while BC2 progenies showed 21-22 chromosomes, and by the BC3 generation, stability was achieved with an average of 20 chromosomes. SSR marker analysis confirmed the progressive reduction of C-genome regions, retaining minimal C-genome-specific bands throughout successive backcrossing. Despite the extensive elimination of C-genome-specific genomic regions, the glyphosate resistance gene from the male parent B. napus was introgressed into BC3 progenies, suggesting that the glyphosate resistance gene located and introgressed in A-chromosome/genome regions of the Brassica plants.

Development of genetically modified rust resistant wheat: A breakthrough by dinted introgression of novel DREB2C and HSFA2 genes under stress induced expression

Wheat is a major staple food worldwide yet numerous yield limiting agents affect its productivity. Stripe rust is a major culprit in this context and efforts have been made to culminate this pathogen using conventional as well as advanced innovative techniques. Transgenic technology is of significant importance in this context and numerous success stories are evident to prove its worth. In the current study, two novel genes HSFA2 and DREB2C were expressed in an elite wheat genotype Akbar, Fakhre-e-Bhakhar under constitutive CAMV35S promoter and stress inducible rd29 Promoters. The shoot cut method was used for the Agrobacterium-mediated transformation and putative transformants were selected on kanamycin 50 mg/L. The resultant transformants were tested through PCR for transgene integration whereas expression analysis was carried out through realtime qPCR. Expression of both of the aforementioned genes was found to be higher under rd29 promoter as compared with transgene(s) expression under CAMV35S promoter. In the bioassay, transgenic wheat plants demonstrated significant tolerance to stress, exhibiting only minor spotting under constitutive expression conditions. Upon exposure to stress, these plants showed exceptional resistance to stripe rust, producing large, bold grains compared to individual trait expressions and negative controls. Subsequently, the DREB2C gene was knocked out to determine if stripe rust control was specifically attributed to this gene. Following the knockout, the onset of stripe rust was comparable to that of the negative control. This led to the conclusion that pyramiding the DREB2C gene with HSFA2 through dual expression represents a novel and highly effective strategy for controlling the widespread stripe rust in wheat. This approach also offers resistance to high temperatures (above 32 °C) from the pollination stage through to maturity.

Contact zone of European (Meles meles Linnaeus, 1758) and Asian (M. leucurus Hodgson, 1847) badgers (Mustelidae, Mammalia) in the rightand left-bank districts of the Saratov region

DNA studies of badgers (Meles sp.) from the right-bank and left-bank areas of the Volga river in the Saratov region are described. Asian badgers (Meles leucurus Hodgson, 1847) inhabit the Left Volga Bank of the Saratov region, while European badgers (M. meles Linnaeus, 1758) inhabit the Right Volga Bank districts of the region, but Asian badgers were found in Khvalynsky district of the Saratov region, besides the European badger. Despite a sufficient number of publications devoted to the Asiatic badger distribution in the Vyatka–Kama region and the Volga region, and studies devoted to the development of systematics of the genus Meles in Russia, the question of the boundaries of the ranges of European and Asiatic badgers and the zones of their sympatry (parapatry) in the Volga–Kama region has not been fully investigated to date. Our work is devoted to the study of this question. As a result of analyzing the biological material collected by us, it was found that all five studied individuals of badgers from the Saratov Volga region phenotypically looked like Asian badgers, but our DNA analysis showed that only two of them were M. leucurus, whilst three ones were heterozygous individuals carrying genes from both species and were identified as hybrids. The remaining 29 individuals were captured in the right-bank areas of the region. Badgers were sampled from individuals from the northern to southern borders of the region in areas located along the Volga river on the Volga upland and in the Oka–Don plain. Of these, one individual from Khvalynsky district turned out to be an Asian badger, one individual from Krasnoarmeysky district was a hybrid of the two named species, and three individuals, one from Tatishchevsky, the second from Volsky and the third from Khvalynsky districts showed introgression of Asian badger genes into the genotype of the European badger. Thus, we have managed to find out that at this stage of development of the phase of the climatic cycle in the Lower Volga region, characterized by warming winters, the Volga river, with its two reservoirs within the Saratov region, is not an absolute zoogeographical boundary, and badgers, whose species are characterized by winter sleep, can in certain conditions overcome, most likely on ice, both the river itself and the lake parts of the Volgograd and Saratov reservoirs. According to the revealed introgression in some individuals from different areas on the Volga upland of the right bank of the Saratov region, it can be assumed that such traveling across the Volga river took place earlier, possibly before its flow was regulated by dams.

Widespread Adaptive Introgression of Major Histocompatibility Complex Genes across Vertebrate Hybrid Zones.

Interspecific introgression is a potentially important source of novel variation of adaptive significance. Although multiple cases of adaptive introgression are well documented, broader generalizations about its targets and mechanisms are lacking. Multiallelic balancing selection, particularly when acting through rare allele advantage, is an evolutionary mechanism expected to favor adaptive introgression. This is because introgressed alleles are likely to confer an immediate selective advantage, facilitating their establishment in the recipient species even in the face of strong genomic barriers to introgression. Vertebrate major histocompatibility complex genes are well-established targets of long-term multiallelic balancing selection, so widespread adaptive major histocompatibility complex introgression is expected. Here, we evaluate this hypothesis using data from 29 hybrid zones formed by fish, amphibians, squamates, turtles, birds, and mammals at advanced stages of speciation. The key prediction of more extensive major histocompatibility complex introgression compared to genome-wide introgression was tested with three complementary statistical approaches. We found evidence for widespread adaptive introgression of major histocompatibility complex genes, providing a link between the process of adaptive introgression and an underlying mechanism. Our work identifies major histocompatibility complex introgression as a general mechanism by which species can acquire novel, and possibly regain previously lost, variation that may enhance defense against pathogens and increase adaptive potential.

English

English

Analysis of the genetic diversity and population structure of Tilia amurensis from China using SSR markers: Implications for conservation

Tilia amurensis is a deciduous broad-leaved tree in the Malvaceae family. It is one of the second-class key protected wild plants in China. The evaluation of genetic polymorphisms of crucial protected species is necessary for conserving germplasm resources. In this study, 15 pairs of highly polymorphic SSR primers were used to analyse the genetic diversity of eight T. amurensis populations and the population structure of nine Tilia populations distributed in China. At the population level (Na = 6.050, Ne = 2.930, I = 1.123, HO = 0.485, HE = 0.523), there was a high level of genetic diversity. The AMOVA results showed that 12 % and 88 % of the total variation occurred among and within populations, respectively. The degree of genetic differentiation was moderate (FST = 0.124), and the level of gene flow was high (Nm = 1.763). The results of UPGMA cluster analysis, PCoA and structure analysis (ΔK = 2) revealed different degrees of gene introgression between the eight T. amurensis populations and Tilia japonica as the outgroup. These findings have important implications for formulating appropriate conservation strategies.

Towards the conservation of the crucian carp in Europe: Prolific hybridization but no evidence for introgression between native and non-native taxa.

Hybridization plays a pivotal role in evolution, influencing local adaptation and speciation. However, it can also reduce biodiversity, which is especially damaging when native and non-native species meet. Hybridization can threaten native species via competition (with vigorous hybrids), reproductive resource wastage and gene introgression. The latter, in particular, could result in increased fitness in invasive species, decreased fitness of natives and compromise reintroduction or recovery conservation practices. In this study, we use a combination of RAD sequencing and microsatellites for a range-wide sample set of 1366 fish to evaluate the potential for hybridization and introgression between native crucian carp (Carassius carassius) and three non-native taxa (Carassius auratus auratus, Carassius auratus gibelio and Cyprinus carpio) in European water bodies. We found hybridization between native and non-native taxa in 82% of populations with non-natives present, highlighting the potential for substantial ecological impacts from hybrids on crucian carp populations. However, despite such high rates of hybridization, we could find no evidence of introgression between these taxa. The presence of triploid backcrosses in at least two populations suggests that the lack of introgression among these taxa is likely due to meiotic dysfunction in hybrids, leading to the production of polyploid offspring which are unable to reproduce sexually. This result is promising for crucian reintroduction programs, as it implies limited risk to the genetic integrity of source populations. Future research should investigate the reproductive potential of triploid hybrids and the ecological pressures hybrids impose on C. carassius.

Genetic Regulatory Perturbation of Gene Expression Impacted by Genomic Introgression in Fiber Development of Allotetraploid Cotton.

Interspecific genomic introgression is an important evolutionary process with respect to the generation of novel phenotypic diversity and adaptation. A key question is how gene flow perturbs gene expression networks and regulatory interactions. Here, an introgression population of two species of allopolyploid cotton (Gossypium) to delineate the regulatory perturbations of gene expression regarding fiber development accompanying fiber quality change is utilized. De novo assembly of the recipient parent (G. hirsutum Emian22) genome allowed the identification of genomic variation and introgression segments (ISs) in 323 introgression lines (ILs) from the donor parent (G. barbadense 3-79). It documented gene expression dynamics by sequencing 1,284 transcriptomes of developing fibers and characterized genetic regulatory perturbations mediated by genomic introgression using a multi-locus model. Introgression of individual homoeologous genes exhibiting extreme low or high expression bias can lead to a parallel expression bias in their non-introgressed duplicates, implying a shared yet divergent regulatory fate of duplicated genes following allopolyploidy. Additionally, the IL N182 with improved fiber quality is characterized, and the candidate gene GhFLAP1 related to fiber length is validated. This study outlines a framework for understanding introgression-mediated regulatory perturbations in polyploids, and provides insights for targeted breeding of superior upland cotton fiber.

African Local Pig Genetic Resources in the Context of Climate Change Adaptation.

Africa is home to a wide diversity of locally adapted pig breeds whose genetic architecture offers important insights into livestock adaptation to climate change. However, the majority of these inherent traits have not been fully highlighted. This review presents an overview of the current state of African pig genetic resources, providing highlights on their population and production statistics, production system, population diversity indices, and genomic evidence underlying their evolutionary potential. The study results reveal an incomplete characterization of local pig genotypes across the continent. The characterized population, however, demonstrates moderate to high levels of genetic diversity, enough to support breeding and conservation programs. Owing to low genetic differentiation and limited evidence of distinct population structures, it appears that most local pig populations are strains within larger breeds. Genomic evidence has shown a higher number of selection signatures associated with various economically important traits, thus making them potential candidates for climate change adaptation. The reportedly early evidence of hybridization with wild suid groups further suggests untapped insights into disease resistance and resilience traits that need to be illuminated using higher-density markers. Nevertheless, gene introgression from commercial breeds is prevalent across Africa; thus, efforts to realize and utilize these traits must increase before they are permanently depleted.

Co-Expression Network Analysis and Introgressive Gene Identification for Fiber Length and Strength Reveal Transcriptional Differences in 15 Cotton Chromosome Substitution Segment Lines and Their Upland and Sea Island Parents.

Fiber length (FL) and strength (FS) are the core indicators for evaluating cotton fiber quality. The corresponding stages of fiber elongation and secondary wall thickening are of great significance in determining FL and FS formation, respectively. QTL mapping and high-throughput sequencing technology have been applied to dissect the molecular mechanism of fiber development. In this study, 15 cotton chromosome segment substitution lines (CSSLs) with significant differences in FL and FS, together with their recurrent parental Gossypium hirsutum line CCRI45 and donor parent G. barbadense line Hai1, were chosen to conduct RNA-seq on developing fiber samples at 10 days post anthesis (DPA) and 20 DPA. Differentially expressed genes (DEGs) were obtained via pairwise comparisons among all 24 samples (each one with three biological repeats). A total of 969 DEGs related to FL-high, 1285 DEGs to FS-high, and 997 DEGs to FQ-high were identified. The functional enrichment analyses of them indicated that the GO terms of cell wall structure and ROS, carbohydrate, and phenylpropanoid metabolism were significantly enriched, while the GO terms of glucose and polysaccharide biosynthesis, and brassinosteroid and glycosylphosphatidylinositol metabolism could make great contributions to FL and FS formation, respectively. Weighted gene co-expressed network analyses (WGCNA) were separately conducted for analyzing FL and FS traits, and their corresponding hub DEGs were screened in significantly correlated expression modules, such as EXPA8, XTH, and HMA in the fiber elongation and WRKY, TDT, and RAC-like 2 during secondary wall thickening. An integrated analysis of these hub DEGs with previous QTL identification results successfully identified a total of 33 candidate introgressive DEGs with non-synonymous mutations between the Gh and Gb species. A common DEG encoding receptor-like protein kinase 1 was reported to likely participate in fiber secondary cell thickening regulation by brassionsteroid signaling. Such valuable information was conducive to enlightening the developing mechanism of cotton fiber and also provided an abundant gene pool for further molecular breeding.

Evaluation of genetic consequences of stocking on the southern-margin populations of white-spotted charr.

Coldwater-adapted freshwater fishes, especially their populations along warm-range margins, are most vulnerable to the climate oscillations associated with global warming. Stocking is a major strategy for avoiding the extinction of these species. However, while stocking can reverse the decline of isolated populations, it may also result in a loss of genetic diversity in the native local population due to the introgressive replacement of hatchery genes. To plan an adequate strategy for conserving locally adapted populations, the genetic impacts of stocking on native lineages should be evaluated from small river branches to wide-ranging drainage areas. We investigated the population genetic structure of white-spotted charr (Salvelinus leucomaenis) within its southern range (Lake Biwa basin, Japan). By applying genome-wide SNP analysis to the population's genetic structure, we assessed the extent of genetic introgression resulting from stocking. White-spotted charr in the Lake Biwa watershed constitutes a distinctive genetic group, within which apparent genetic differentiation was observed. The hatchery-reared fish line commonly used for supplementation stocking in the catchment was discernable from the native population, enabling us to analyze genetic introgression across the entire drainage area. Admixed individuals resulting from hatchery introgression were observed in most of the stocked sites that showed relatively high heterozygosity and nucleotide diversity. However, their genetic differentiation was much lower than that of native populations. The supplementation history as well as the road availability contributed substantially to the introgression of hatchery genes. Populations with the native genetic structure remained in the upstream regions of the tested rivers. However, their heterozygosity and nucleotide diversity were low when compared with that of the populations with hatchery supplementation. Our results shed light on the genetic impacts of stocking on isolated native populations and suggest that conventional supplementation methods cannot preserve a unique biodiversity in the distribution margin.

De novo assembly and comprehensive analysis of the mitochondrial genome of Taxus wallichiana reveals different repeats mediate recombination to generate multiple conformations

Taxus plants are the exclusive source of paclitaxel, an anticancer drug with significant medicinal and economic value. Interspecies hybridization and gene introgression during evolution have obscured distinctions among Taxus species, complicating their phylogenetic classification. While the chloroplast genome of Taxus wallichiana, a widely distributed species in China, has been sequenced, its mitochondrial genome (mitogenome) remains uncharacterized.We sequenced and assembled the T. wallichiana mitogenome using BGI short reads and Nanopore long reads, facilitating comparisons with other gymnosperm mitogenomes. The T. wallichiana mitogenome spanning 469,949 bp, predominantly forms a circular configuration with a GC content of 50.51%, supplemented by 3 minor configurations mediated by one pair of LRs and two pairs of IntRs. It includes 32 protein-coding genes, 7 tRNA genes, and 3 rRNA genes, several of which exist in multiple copies.We detailed the mitogenome's structure, codon usage, RNA editing, and sequence migration between organelles, constructing a phylogenetic tree to elucidate evolutionary relationships. Unlike typical gymnosperm mitochondria, T. wallichiana shows no evidence of mitochondrial-plastid DNA transfer (MTPT), highlighting its unique genomic architecture. Synteny analysis indicated extensive genomic rearrangements in T. wallichiana, likely driven by recombination among abundant repetitive sequences. This study offers a high-quality T. wallichiana mitogenome, enhancing our understanding of gymnosperm mitochondrial evolution and supporting further cultivation and utilization of Taxus species.

Effect of Introgression of Ty-1 and ty-5 Genes on Productivity, Quality, and Antioxidant Compounds in De la Pera Tomato Breeding Lines

Tomato (Solanum lycopersicum L.) is a crop that is affected by more than a hundred viral species. De la pera is a local varietal type of tomato that is very popular in southeastern Spain. However, it is highly susceptible to several viruses, such as Tomato yellow leaf curl virus (TYLCV), which is considered one of the most important diseases of tomato crops and is a limiting factor for production in both outdoor and protected crops, making it difficult to eradicate. This study shows the effect of gene introgression on the performance of traditional lines of De la pera by combining two genes that offer tolerance to TYLCV, Ty-1 and ty-5, on some yield and quality traits and on the antioxidant capacity of tomato fruits. Two pear tomato breeding families, UMH175 and UMH220, were evaluated. Four lines from each of the families with all homozygous combinations of the Ty-1 and ty-5 genes were studied. The results showed that the introgression of the ty-5 allele produced a slight negative effect on yield, mean fruit weight, total soluble solids, and titratable acidity, in contrast to Ty-1, which produced a large negative effect. None of the introgressions showed a negative effect on the antioxidant compounds. ty-5 is a promising gene for use in breeding programs.

Biased gene introgression and adaptation in the face of chloroplast capture in Aquilegia amurensis.

Chloroplast capture, a phenomenon that can occur through interspecific hybridization and introgression, is frequently invoked to explain cytonuclear discordance in plants. However, relatively few studies have documented the mechanisms of cytonuclear coevolution and its potential for driving species differentiation and possible functional differences in the context of chloroplast capture. To address this crucial question, we chose the Aquilegia genus, which is known for having minimal sterility among species, and inferred that A. amurensis captured the plastome of A. parviflora based on cytonuclear discordance and gene flow between the two species. We focused on the introgression region and its differentiation from corresponding regions in closely related species, especially its composition in a chloroplast capture scenario. We found that nuclear genes encoding cytonuclear enzyme complexes (CECs; i.e., organelle-targeted genes) of chloroplast donor species were selectively retained and displaced the original CEC genes in chloroplast-receiving species due to cytonuclear interactions during introgression. Notably, the intrinsic correlation of CEC introgression was a greater degree of evolutionary distance for these CECs between A. amurensis and A. parviflora. Terpene synthase activity genes (GO: 0010333) were overrepresented among the introgressed genes, and more than 30% of these genes were CEC genes. These findings support our observations that floral terpene release pattern is similar between A. amurensis and A. parviflora compared with A. japonica. Our study clarifies the mechanisms of cytonuclear coevolution, species differentiation and functional differences in the context of chloroplast capture and highlights the potential role of chloroplast capture in adaptation.

Improvement of superior soybean variety, Biosoy-1 for aluminium tolerance character

Abstract Indonesia has lot of sub-optimal land, especially outside Java, but generally the land is acidic, contains lots of heavy metals and is poor in nutrients, making it less suitable for agriculture, including soybean cultivation. Efforts to improve land conditions through the application of liming are quite helpful, but are inefficient because they are easily washed out by rainwater and require expensive labor and costs for large areas. The use of tolerant and adaptive varieties for acidic land are effective solutions. Biosoy-1 and Biosoy-2 are new superior soybean varieties released by Ministry of Agriculture which have high yield potential (more than 3 tons/ha) and big grain, but are less adaptive to sub-optimal land so that the planting area is still limited. Efforts to improve the Biosoy variety for aluminum stress tolerant have been carried out through the introgression of the MaMt2 gene from transgenic soybean lines into the Biosoy variety. Thirty of F1 soybean seeds have been produced and 24 plants of them were positive for carrying the MaMt2 gene. Furthermore, the F1-MaMt2 plants were backcrossed to Biosoy several times in order to obtain a soybean line with high yield and tolerance to aluminum stress. Currently, a total of 16 number of BC3F1 seeds are being planting in confined screen house for molecular analysis and following by backcrossing to Biosoy-1 variety to produce BC4F1 seeds.