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Understanding the genetic diversity of crops is of fundamental importance for the efficient use and improvement of germplasm resources. Different molecular genotyping systems have been implemented for population structure and phylogenetic relationships analyses, among which, microsatellites (SSRs) and single nucleotide polymorphisms (SNPs) markers have been the most widely used. This study reports the efficacy of SNPs detected via double-digest restriction-site-associated DNA sequencing (ddRADseq) and SSRs analyzed via capillary electrophoresis (CE) and high-resolution melting (HRM) in tomato. In total, 21,020 high-quality SNPs, 20 CE-SSRs, and 17 HRM-SSR markers were assayed in a panel of 72 accessions that included a diversified set of landraces, long-shelf-life cultivars and heirlooms with different origins and fruit typology. The results showed how the population structure analysis was consistent using the three genotyping methods, although SNPs were more efficient in distinguishing cultivar types and in measuring the degree of accessions' similarity. Compared to CE-SSR, the analysis of microsatellites via HRM yielded a slightly higher number of alleles (98 vs. 96). HRM-SSR demonstrated a distinction between European and non-European germplasm, better resolving the collection's diversity and being more consistent with SNP data. Phylogenetic trees drawn with independent marker data, detected specific groups of accessions showing robust clusters, highlighting how heirlooms were less heterogeneous than landraces. In addition, the fixation index (FST) revealed a high genetic differentiation between heirlooms and long-shelf-life cultivars, with SNP and SSR-HRM data emphasizing the distinction between cherry and plum types and CE-SSR data between cherry and oxheart types. In all instances, a greater molecular variance was found within the different considered biological statuses, provenances, and typologies rather than among them. This work presents the first attempt to compare the three tomato genotyping techniques in tomato. Findings highlighted how the markers used are complementary for genetic diversity analysis, with SNPs providing better insight and HRM-SSR as a viable alternative to capillary electrophoresis to dissect the genetic structure. [ABSTRACT FROM AUTHOR]

The All of Us Research Program (AoU) is an initiative designed to gather a comprehensive and diverse dataset from at least one million individuals across the USA. This longitudinal cohort study aims to advance research by providing a rich resource of genetic and phenotypic information, enabling powerful studies on the epidemiology and genetics of human diseases. One critical challenge to maximizing its use is the development of accurate algorithms that can efficiently and accurately identify well-defined disease and disease-free participants for case-control studies. This study aimed to develop and validate type 1 (T1D) and type 2 diabetes (T2D) algorithms in the AoU cohort, using electronic health record (EHR) and survey data. Building on existing algorithms and using diagnosis codes, medications, laboratory results, and survey data, we developed and implemented algorithms for identifying prevalent cases of type 1 and type 2 diabetes. The first set of algorithms used only EHR data (EHR-only), and the second set used a combination of EHR and survey data (EHR+). A universal algorithm was also developed to identify individuals without diabetes. The performance of each algorithm was evaluated by testing its association with polygenic scores (PSs) for type 1 and type 2 diabetes. We demonstrated the feasibility and utility of using AoU EHR and survey data to employ diabetes algorithms. For T1D, the EHR-only algorithm showed a stronger association with T1D-PS compared to the EHR + algorithm (DeLong p-value = 3 × 10−5). For T2D, the EHR + algorithm outperformed both the EHR-only and the existing T2D definition provided in the AoU Phenotyping Library (DeLong p-values = 0.03 and 1 × 10−4, respectively), identifying 25.79% and 22.57% more cases, respectively, and providing an improved association with T2D PS. We provide a new validated type 1 diabetes definition and an improved type 2 diabetes definition in AoU, which are freely available for diabetes research in the AoU. These algorithms ensure consistency of diabetes definitions in the cohort, facilitating high-quality diabetes research. [ABSTRACT FROM AUTHOR]

Abscisic acid (ABA) is a key plant hormone that regulates plant growth and response to stress. Pyrabactin resistance 1-like (PYR/PYL) proteins are ABA receptors involved in the initial steps of ABA signaling. Triticum monococcum L. subsp. aegilopoides is an important germplasm resource for wheat. In this study, we identified 15 PYL genes from T. monococcum L. subsp. aegilopoides and found that they were distributed across five chromosomes. Based on phylogenetic analysis, we classified these genes into three subfamilies. Members of each subfamily have similar gene structures and contain a common motif. Further analysis revealed that the promoters have multiple hormone-related elements. We found 7, 33, and 49 collinear gene pairs in three different ploidy wheat species (T. urartu, T. turgidum and T. aestivum), indicating that PYL genes are relatively conserved during the process of wheat polyploidization. Additionally, interaction networks and miRNA targets were predicted, revealing interactions between PYL proteins and key components of the abscisic acid signaling network. miR9666b-3p may serve as a central factor in PYL involvement in the abscisic acid network. Through RNA-seq analysis and qPCR validation, three genes (TbPYL2, TbPYL5, and TbPYL12) were found to potentially play a role in cold stress. These findings lay the groundwork for further research on PYL genes in T. monococcum L. subsp. aegilopoides. [ABSTRACT FROM AUTHOR]

Flowering time of crops is critical for maximizing yield, quality and regional adaptability under target environments. In rice, Heading date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1) proteins are the key factors of flowering time regulation in the florigen activation complex. However, effects of hd3a and rft1 mutations on the flowering time under long-day conditions are not clear. In this study, we generated single and double mutants of Hd3a and RFT1 in japonica varieties Shen Nong 9816 (SN9816) background, termed hd3a-SNs, rft1-SNs and doub-SNs, by using CRISPR/Cas9 system. The flowering time of hd3a-SN mutants was similar to wild-type (WT); but mutations of RFT1 delayed flowering time by 11 to 14 days comparing to WT under nature long day (NLD) conditions. Double mutants of Hd3a and RFT1 (doub-SNs) exhibited an extremely late flowering phenotype, and they did not flower up to 365 days after regeneration under either NLD or short-day conditions. The leaf emergency rate of RFT1 mutants was similar to WT, suggesting that the late flowering phenotype of rft1-SNs was caused by delayed floral transition, but not by retarded growth. The expression of the key floral organ identity genes was significantly decreased in rft1-SN and doub-SN mutants, resulting in late flowering phenotypes. The expression profiles, evolution and haplotypes of Hd3a and RFT1 was also analyzed. Our studies provide insight into the potential utilization of Hd3a and RFT1 gene resources to improving growth period and regional adaptability in rice breeding. [ABSTRACT FROM AUTHOR]

Lanternfish not only boast the most abundant biomass among marine fish species but also play a vital role in marine ecosystems. As one of the lanternfish species with the highest global catch, the skinnycheek lanternfish (Benthosema pterotum) is widely distributed in the Indo-Pacific region, playing a pivotal role in the marine biological pump. This study constructed the first chromosome-level genome of B. pterotum using a combination of short-read sequencing, PacBio, and Hi-C sequencing technologies. The genome size of B. pterotum is 1,272.53 Mb, with a contig N50 of 810 Kb and a scaffold N50 of 54.49 M. More than 99.65% of contigs were successfully anchored onto 24 pseudochromosomes, and 95.7% of BUSCO genes were identified within the genome, demonstrating the high level of completeness in genome assembly. A total of 24,934 protein-coding genes were predicted, of which 99.02% were functionally annotated. The successful assembly of a high-quality genome for B. pterotum provides valuable genetic resources for better understanding its biological characteristics and potentially those of all lanternfish species. [ABSTRACT FROM AUTHOR]

Identification of high carotenoid germplasm is crucial to assist breeders in provitamin-A biofortification of sorghum (Sorghum bicolor [L.] Moench). High-performance liquid chromatography is the gold standard for carotenoid quantification, however, it is not feasible for large scale phenotyping due to its high cost and low throughput. In this study, we tested the feasibility of using grain color as a high-throughput method of carotenoid biofortification breeding. We hypothesized that visual, color-based selection can be an effective strategy to identify high-carotenoid accessions. Yellow grain had significantly higher carotenoid content than red, brown, and white grain. The degree of yellowness could distinguish the presence or absence of carotenoids, but could not distinguish carotenoid concentrations within yellow-only accessions. The degree of luminosity of the grain, however, was able to better predict carotenoid concentrations within yellow-only accessions. Genome-wide association studies identified significant marker-trait associations for qualitative and quantitative grain color traits and carotenoid concentrations near carotenoid pathway genes—ZEP, PDS, CYP97A, NCED, CCD, and LycE—three of which were common between grain color and carotenoid traits. These findings suggest that using grain color as a method for screening germplasm may be an effective high-throughput selection tool for prebreeding and early-stage breeding in carotenoid biofortification. [ABSTRACT FROM AUTHOR]

Sea cucumbers are deposit feeding members of marine benthic communities. The over-exploitation of sea cucumber natural stocks, especially in the Mediterranean basin, is having negative impacts on the marine ecosystem. This concerns had led the Italian government to take legal actions to preserve these important marine resources. The aim of this study was to evaluate the level of genetic diversity and population structures within two sympatric Holothuria sea cucumber species, H. polii and H. tubulosa, across ten Mediterranean areas along Italy. A 323 bp portion of the COI mitochondrial gene was sequenced in a total of 441 holothurians (251 H. polii, 177 H. tubulosa and 13 from other species). Genetic diversity analyses and analysis of molecular variance (AMOVA) suggest that H. polii and H. tubulosa species are distinct, but within and among populations are homogeneous, indicating active gene flows across the Mediterranean areas investigated. H. polii showed a lower genetic diversity than H. tubulosa, probably related to differences in life history traits. Phylogenetic analyses showed a clear differentiation between the two species, even if six specimens morphologically assigned to a species clustered within the other species, indicating a possible occurrence of hybridization events. These data will be useful in implementing conservation actions for these holothurian genetic resources. [ABSTRACT FROM AUTHOR]

Bract coloration is one of the key ornamental traits in Bougainvillea, yet research has predominantly focused on phenotypic color traits and pigment composition, with limited understanding of the molecular mechanisms underlying color formation. This gap hinders the improvement and innovation in bract coloration. To elucidate the regulatory mechanisms of bract coloration in Bougainvillea and to enhance the utilization of its germplasm resources, this study employed the Illumina Novaseq 6000 sequencing platform to conduct transcriptomic sequencing on 21 samples of bracts exhibiting seven distinct phenotypes. Comparative analysis against Nr, Pfam, EggNOG, GO, and KEGG databases annotated 90,279 unigenes. The highest annotation rates were achieved with the Nr (40.13%), GO (30.44%), and EggNOG (25.64%) databases. Among the species annotated, Beta vulgaris (20.08%) and Chenopodium quinoa (14.58%) shared the highest homology with Bougainvillea bract transcriptomes. WGCNA analysis identified 12 positively correlated tissue-specific modules, of which 2 are related to bract color formation. By comparing transcriptome data and genes within these specific modules against the KEGG database, a total of 321 unigenes associated with bract color formation in Bougainvillea were discovered. Among these, 220 unigenes are involved in anthocyanin synthesis, 43 unigenes are involved in betalain synthesis, 23 unigenes are annotated as Chlorophyll a-b binding protein genes, and 35 unigenes participate in carotenoid synthesis. Quantitative real-time PCR (qRT-PCR) validation of 16 differentially expressed genes (DEGs) including PAL2, CHS1, ANS, BZ1, 6GT, CDOPA5GT, ANR, CHS2, and DOPA, revealed significant expression differences among magenta, yellow, white, and cherry-colored bracts, suggesting their potential as candidate genes for bract color development. This study not only enriches the transcriptomic data of Bougainvillea but also identifies genes associated with bract coloration, providing a valuable theoretical basis for future gene cloning, genetic engineering, and breeding efforts in Bougainvillea. [ABSTRACT FROM AUTHOR]

Ulomoides dermestoides, a member of the Tenebrionidae family, is known by various common names such as Chinese beetle, Chinese weevil, peanut beetle, cancer beetle, or asthma beetle. Despite its origin in Asia, it has achieved global distribution owing to its perceived medicinal properties. In this study, we employed a combination of Illumina short-read, PacBio long-read, and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to produce a high-quality, chromosome-scale genome assembly of U. dermestoides. The assembled genome spans 253.38 Mb across 11 chromosomes, including the two sex chromosomes, X and Y. Key metrics include contig and scaffold N50 values of 9.83 Mb and 28.62 Mb, respectively, with an estimated genome completeness of 99.62%. Annotation efforts identified 15,553 protein-coding genes and revealed that 48.11% of the genome comprises repetitive sequences. This meticulously assembled genome serves as a pivotal resource for elucidating the genetic determinants underlying the species' ecological habits and potential medicinal properties. [ABSTRACT FROM AUTHOR]

Reaumuria soongarica is a xerophytic shrub belonging to the Tamaricaceae family. The species is widely distributed in the deserts of Central Asia and is characterized by its remarkable adaptability to saline and barren desert environments. Using PacBio long-read sequencing and Hi-C technologies, we assembled a chromosome-level genome of R. soongarica. The genome assembly has a size of 1.28 Gb with a scaffold N50 of 116.15 Mb, and approximately 1.25 Gb sequences were anchored in 11 pseudo-chromosomes. A completeness assessment of the assembled genome revealed a BUSCO score of 97.5% and an LTR Assembly Index of 12.37. R. soongarica genome had approximately 60.07% repeat sequences. In total, 21,791 protein-coding genes were predicted, of which 95.64% were functionally annotated. This high-quality genome will serve as a foundation for studying the genomic evolution and adaptive mechanisms to arid-saline environments in R. soongarica, facilitating the exploration and utilization of its unique genetic resources. [ABSTRACT FROM AUTHOR]

Global climate change poses challenges to agricultural production and food security. Assessing the adaptive capacity of crop wild relatives to future climate is important for protecting key germplasm resources and breeding new crops. We performed population genomics, genotype-environment association analyses, and genomic offset assessment of Chinese wild rice, Zizania latifolia, a crop wild relative and potential new grain crop, based on 168 individuals from 42 populations. We found two genetic lineages in Z. latifolia, corresponding to the south and north of its range, that diverged during the Late Pleistocene. We also identified lineage-specific positively selected genes associated with flower development and flowering, seed shattering, pathogen defense response and cold tolerance. We further found that populations from southeastern China are the most maladapted to future climate and should be prioritized for conservation. Our findings provide important clues for leveraging existing genetic diversity to identify important germplasm resources and create climate-resilient crops. A landscape genomics analysis of Chinese wild rice identifies signatures of local adaptation in its two lineages and the most maladapted populations under future climate conditions, and provides important clues for its conservation and use. [ABSTRACT FROM AUTHOR]

Pampus argenteus is a highly commercial marine fish whose population is declining sharply. Here, we generated a female P. argenteus genome, spanning 536.33 Mb with contig N50 of 1.79 Mb; 24070 genes (99.50% of 24,182) were functionally annotated. To improve quality of it, we assembled a 553.79 Mb genome of male fish with contig N50 of 24.75 Mb through HiFi and ultra-long ONT sequence technologies; 550.82 Mb were anchored onto 24 gap-free chromosomes; 22,892 genes (98.1% of 23,346) were functionally annotated; the QV value was 51.55 with 98.9% of BUSCO and 99.39% coverage of Illumina reads. Finally, we compared this genome with previous published one, revealing 37,301 SVs. 52.82 Mb and 18.05 Mb SDs were characterized in our and published assemblies, respectively, and 48.96 Mb PURs were constructed. Thus, this genome assembly exhibits excellent completeness, continuity and accuracy comparing to the published one, which can be current preferred reference genome. Overall, these works help aquaculture and wild resources recovery of P. argenteus and provide a valuable genetic resource for study. [ABSTRACT FROM AUTHOR]

The genetic analysis of potato is hampered by the complexity of tetrasomic inheritance. An ongoing effort aims to transform the clonally propagated tetraploid potato into a seed-propagated diploid crop, which would make genetic analyses much easier owing to disomic inheritance. Here, we construct and report the large-scale genetic and heterotic characteristics of a diploid F2 potato population derived from the cross of two highly homozygous inbred lines. We investigate 20,382 traits generated from multi-omics dataset and identify 25,770 quantitative trait loci (QTLs). Coupled with gene expression data, we construct a systems-genetics network for gene discovery in potatoes. Importantly, we explore the genetic basis of heterosis in this population, especially for yield and male fertility heterosis. We find that positive heterotic effects of yield-related QTLs and negative heterotic effects of metabolite QTLs (mQTLs) contribute to yield heterosis. Additionally, we identify a PME gene with a dominance heterotic effect that plays an important role in male fertility heterosis. This study provides genetic resources for the potato community and will facilitate the application of heterosis in diploid potato breeding. An ongoing effort aims to transform the clonally propagated tetraploid potato to a seed-propagated diploid crop, but our understanding of it disomic inheritance is limited. Here, the authors report genetic basis of heterosis in the elite hybrid potato and identify a male fertility-related PME gene with dominance heterotic effect. [ABSTRACT FROM AUTHOR]

This study used high-throughput phenotyping data analysis to examine 64 Tartary buckwheat (Fagopyrum tataricum Gaertn.) germplasm accessions with 5787 samples. The focus is on understanding correlations between seed traits such as seed area, width, height, circularity, and roundness, and their potential implications for breeding. The results revealed a positive correlation between seed area, width, and height, while no correlation was found between seed area, width, height, and circularity or roundness. These findings contradicted the initial hypotheses, which suggested that circular seeds would have a larger area and that roundness would positively correlate with seed area. Instead, at least the genetic resources in this study showed that the square shape of buckwheat seeds would be large. Subsequent analysis of germplasm accessions' traits revealed that the largest seed area accession was IT199282, while the smallest was IT310559. Interestingly, IT310559 ranked relatively high in circularity, prompting two new hypotheses. First, it was suggested that breeders have not yet developed these collected germplasms, meaning that there has been no selection pressure for larger seeds. Second, it was hypothesized that if selection pressure were applied to larger seeds, the seed shape might change to a more circular form compared to natural conditions. In conclusion, the high-throughput data analysis in the current study helped identify the phenotypic diversity of Tartary buckwheat seeds and provided insights into breeding larger seeds that have not been previously explored. [ABSTRACT FROM AUTHOR]

Soybean is an indispensable crop producing the majority of vegetative oils and proteins. China has been importing millions of ton of soy beans in recent years. Developing new varieties with favorable traits in both yield and resilience has great potential to meet the market needs in China. In this study, we bred a new variety (Xiangchun 37) which has been licensed by Ministry of Agriculture and Rural Affairs of the People's Republic of China in 2024. In the field tests, Xiangchun 37 showed medium maturity period (107.4 days from sowing to harvest), high yield (187.3 kg/667m2), and high seed oil content (22.19%). Overall assessment showed Xiangchun 37 had other favorable traits including the plant architecture and disease resistance. In conclusion, Xiangchun 37 is a new variety suitable for Hunan Province, China and has promising future for further genetic improvement as a germplasm with multiple favorable traits. [ABSTRACT FROM AUTHOR]

In the current context of climate change, marked by severe drought and heat stresses, we hypothesized that the trait plasticity, opposite of stability, could be an important mechanism of reaching adaptability and therefore enhancing resilience. To assess this, we tested 10 promising genotypes under three environments (E1, E2, and E3) for yield and its components: Number of Spikes per m2 (NS/m2), Number of Spikelets per Spike (NSpk/S), Number of Grains per Spikelet (NG/Spk), Number of Grains per Spike (NG/S), Number of Grains per m2 (NG/m2); and Thousand Grain Weight (TGW). A highly significant effect (p < 0.01) of the environment (E) was observed for all traits. Additionally, a significant effect (p < 0.05) of genotype (G) was identified in all traits except TGW. While a significant effect (p < 0.05) of genotype by environment interaction (G×E) was noted for NSpk/S and TGW. The stability and plasticity criteria were reported as a positive way to achieve adaptability when they reflect a high yielding potential of stable or plastic traits. As depicted by GGE- analysis, the best stable genotypes with high performance were Kharouba for NS/m2, NG/S, and NG/m2, Amal for NG/S, 15/42, Malika, and 90-55-17 for NSpk/S, Achtar for NG/Spk, and 15/49 for TGW. While the plastic genotypes with high performance were 15/42 for NS/m2, Achtar for NG/S and NG/m2, Amal for NSpk/S and NG/Spk, and 90–55-17 for TGW. These genotypes that combine stability or plasticity criteria with high yielding performances hold promise as potential genetic resources in breeding programs aiming to achieve desirable yield component structure for better adaptability and resilience. [ABSTRACT FROM AUTHOR]

In order to determine the diversity in local seedling origin mango genotypes from different five districts (Navsari, Valsad, Dang, Tapi and Surat) of South Gujarat region during 2021–2023, which have been found in orchards or backyards by using IPGRI mango descriptor. The exploration of genetic resources was carried out to find alternative genotype against prevailing varieties in the state and it sustain mango production in future. A total of 113 mango seedlings were identified and characterized on basis of 7 qualitative, 12 quantitative and 6 biochemical parameters using Completely Randomized Design with three replications of quantitative characteristics. High variation among genotypes was observed with respect qualitative, quantitative and biochemical parameters. Ten superior genotypes were identified based on five commercially important traits viz., fruit weight (> 200 g), pulp percentage (> 60.00%), TSS (> 20 °Brix), shelf life (> 7 days) and overall acceptability (> 7 point). The genetic variability revealed that higher heritability coupled with higher genetic advance as per cent of mean for 12 quantitative characteristics namely mature fruit weight, fruit length, fruit width, pulp weight, peel weight, stone weight, TSS, acidity, ascorbic acid, total sugars, reducing sugars and non-reducing sugars. The First three Principal component contributed 70.21% of total variation and characters such as mature fruit weight, fruit length, fruit width, pulp weight, peel weight and stone weight most contributing towards diversity in germplasm. Hierarchical cluster analysis resulted the genotypes was grouped into three clusters and genotypes present in cluster III (20) and cluster I (39) had found most divers from each other. [ABSTRACT FROM AUTHOR]

Safflower oil with high oleic is an important source of oil due to its oxidative stability and nutritional value as well as its industrial benefits. Identification of molecular markers associated with oil quality traits may aid in genotype selection in breeding efforts of safflower. To determine the genetic basis of seed oil, oleic acid, and linoleic acid content in safflower seeds, a recombinant inbred population was developed from a cross between Goldasht (low oleic line) and Mex 22–191 (high oleic line) by individual self-pollinated plants in each generation (from F2 to F9). Fatty acid components were detected by gas chromatography and subsequently analyzed by QTL analysis. The high variability in fatty acid composition was demonstrated and the first high-oleic safflower genotype was generated. A new linkage map with 69 AFLP and 45 ISSR polymorphic markers was made, covering 1472,441 cM of the safflower genome. A total of 63 individual QTLs and 238 epistatic QTLs, related to oil quality, were detected in 14 genomic regions. Some major QTLs with phenotypic variation greater than 10% were identified for the measured traits. These results demonstrate that major QTL may play an important role in increase the oleic acid of the genetic material used. Furthermore, the larger number of minor QTLs and epistatic QTLs, both of which have additive effects, indicates that the expression of these traits is also influenced by interactions between multiple genes. Our results provide additional genetic resources that can be used to precisely breed these traits in the future. [ABSTRACT FROM AUTHOR]

Solanum microdontum (mcd) is a tuber-bearing relative of commercial potato. Although wild, it has many attractive traits for breeding. Previous research has shown it has exceptional ability to sequester calcium in its tubers, a trait associated with tuber disease resistance and tuber quality. We used a set of mcd from 50 populations in the US Potato Genebank (USPG) shown to encompass most of the genetic diversity in the species, two individuals from each population. Tubers were produced in pots in the USPG greenhouse in two years, and freeze dried samples tested for calcium content. Some exceptionally high Ca accumulators were identified (especially clone mcd40B1 from PI 473166). Because other minerals were measured in the same tests, the highest accumulators for K, Mg, Zn in mcd were also identified. All the stocks tested are available in vitro from USPG for additional research and breeding. [ABSTRACT FROM AUTHOR]

Zebra chip is an increasingly serious disease in commercial potato production globally. Resistance can be pursued by control of the insect vector, the tomato-potato psyllid, Bactericera cockerelli or the bacterial causal agent, Candidatus Liberibacter solanacearum (Lso). Some Lso-infected plants of the wild potato species S. microdontum (mcd) had been observed to have low symptom expression. Thus, we evaluated a representative core collection of 86 individuals from 50 mcd populations in the US Potato Genebank (USPG). Real-time quantitative PCR on tissue from infected leaves was used as a proxy for bacterial titer of Lso. Russet Burbank control had 56% of the MLT of the most susceptible mcd individual. The average for all mcd was 67%, and the lowest, most resistant six mcd individuals were 0%. Repeated testing of those six individuals identified two as most reliably resistant: mcd15B2 from PI 265575 and mcd62B1 from PI 498126. All of these mcd individuals are available from USPG. They should be useful for research and breeding aimed at better understanding and controlling Zebra chip disease. [ABSTRACT FROM AUTHOR]

Genetic characterization and its association with quantitative traits in local breeds are important tools for the genetic improvement and sustainable management of animal genetic resources. Myogenic regulatory factor 5 (MYf5) and POU class 1 homeobox 1 (POU1F1) are candidate genes which play important roles in growth and development of mammals. The present study aims to detect the genetic diversity of the MYf5 and POU1F1 genes in four local Egyptian rabbit breeds and their association with growth traits, using PCR-restriction enzyme (PCR–RFLP), PCR-single-strand conformational polymorphism (PCR–SSCP), and direct sequencing techniques. The results showed that MYF5 exon 1 was observed with two genotypes in Baladi Black (BB), Gabali (GB) and New Zealand White (NZW) breeds while APRI-line (APRI) presented one genotype. The genetic diversity of Myf5 exon 2 between breeds showed two genotypes in APRI compared to three in NZW and four genotypes in BB and GB breeds. The genetic diversity of the POU1F1 gene (intron 5 and partial cds) in different rabbit breeds was two genotypes in NZW and three genotypes in BB, GB, and APRI breeds with different frequencies for each genotype. Based on the statistically significant difference between genes genotypes and growth weight, the results suggested that the genotypes of Myf5 exon 2 (1 and 2) of the BB breed, Myf5 exon 2 genotype 2 of the APRI breed, and genotype 1 of Myf5 exon 1 and genotype 1 of POU1F1 of the NZW breed compared to genotypes for each gene can be considered candidate molecular markers associated with the improvement of growth traits in these breeds. [ABSTRACT FROM AUTHOR]

The olive is an economically important and indispensable species of the Mediterranean basin with remarkable historic and cultural significance. Wild olives constitute a priceless reservoir of genetic diversity which has great value for olive breeding and conservation programs. However, global climate changes especially global warming is expected to threaten olive cultivation in future causing large economic loses in the region. Therefore, knowledge about distribution and abundance of wild olive populations is important to maximize their conservation, safeguard, and exploitation. Muğla province, where the wild olives make up an important part of the vegetation, is one of the main olive producing area in Turkey with many towns and villages dependent on the olive. In this study, our aim is to examine the current geographical distribution and density of wild olive populations in this province and the 82 islands around its coast. The results demonstrated that young olives, which show good adaptation to region, just have started to expand to the higher parts of the Kavaklıdere district. In addition, in most of the islands wild olives are preserved in their undisturbed natural habitats where they exist as small groves or scattered plants. The results of this study provides important insights for the conservation of wild olive genetic resources. The data reported here, are based on actual field data thus the geographic coverage tends to be complete and consistent. [ABSTRACT FROM AUTHOR]

Tetraploid oysters are valuable germplasm resources for the production of triploid oysters. However, the broodstock condition and gonadal development of tetraploid oysters are poorly understood. To assess the effects of temperature on gamete quantity and quality, tetraploid and diploid oysters were held at controlled temperatures of 18, 20 and 22 °C for 120 days. The gametogenesis process in tetraploid and diploid oysters showed an accelerated trend in response to increased conditioning temperatures. Nonetheless, the gonadal development of tetraploid oysters was slower than that of diploid oysters. Histomorphometric analysis of gonadal tissues showed variations in observed sex ratio under different conditioning temperatures. The proportions of tetraploid and diploid males increased with elevated temperature. However, survival rates of tetraploid and diploid oysters at 22 °C were significantly lower than those at 18 and 20 °C (P < 0.05). In terms of the number of oocytes and spermatozoa, tetraploid oysters were fewer than diploid oysters. Overall, these results demonstrated the differences in broodstock conditioning and gonadal development between tetraploid and diploid oysters, suggesting the need for specialized broodstock cultivation strategies for tetraploid oysters. [ABSTRACT FROM AUTHOR]

Pathogenesis-related protein 10 (PR10) family genes play a crucial role in plant defense against various stressors. However, gene member and function identification of PR10 family in sugarcane remain largely unexplored. This study systematically identified and characterized this family genes in Saccharum spontaneum genome as well as their transcriptional expression in two sugarcane cultivars in response to infection by pathogenic bacteria Xanthomonas albilineans (Xa) and Acidovorax avenae subsp. avenae (Aaa) and foliar application of exogenous salicylic acid (SA). A total of 24 SsPR10 family genes were identified and categorized into two subfamilies, i.e., IPR10 (SsIPR10-1–14) and NCS (SsNCS-1–10). Six and two sets of SsPR10 underwent tandem and fragmental duplication events, respectively. RNA sequencing dataset and quantitative RT-PCR assay uncovered that ShIPR10-1/2/4/7/11/12 and ShNCS-8 genes were dramatically upregulated with increases of 3.2–107.2-fold in LCP85-384 (resistant to leaf scald), while they were slightly upregulated with increases of 1.26–7.1-fold in ROC20 (susceptible to leaf scald) for 24–72 h post inoculation under Xa infection. ShIPR10-1/7/12 and ShNCS-8 were significantly upregulated in both cultivars triggered by Aaa infection with increases of 2.4–21.0-fold. Under exogenous salicylic acid treatment, ShIPR10-1/2/4/7/11/12 were remarkably upregulated by 3.6–6.1-fold in LCP85-384 at 12 h post treatment (hpt) but were downregulated by 81.3% in ROC20 at 24 hpt, as compared to the control 0 hpt. In addition, ShNPR1 and ShPR1 involved in the SA signal transduction pathway displayed positive roles in sugarcane under both bacterial attacks and SA treatment. Collectively, our data provide important genetic resources for improving sugarcane tolerance to pathogenic bacterial stress and disease-resistance breeding in sugarcane for food security. [ABSTRACT FROM AUTHOR]

Although advances in long-read sequencing technology and genome assembly techniques have facilitated the study of genomes, little is known about the genomes of unique Chinese indigenous breeds, including the Huai pig. Huai pig is an ancient domestic pig breed and is well-documented for its redder meat color and high forage tolerance compared to European domestic pigs. In the present study, we sequenced and assembled the Huai pig genome using PacBio, Hi-C, and Illumina sequencing technologies. The final highly contiguous chromosome-level Huai pig genome spans 2.53 Gb with a scaffold N50 of 138.92 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score for the assembled genome was 95.33%. Remarkably, 23,389 protein-coding genes were annotated in the Huai-pig genome, along with 45.87% repetitive sequences. Overall, this study provided new foundational resources for future genetic research on Chinese domestic pigs. [ABSTRACT FROM AUTHOR]

The Cape hare (Lepus capensis) is among the most widely distributed hare species globally, inhabiting extensive regions across Africa, the Middle East, and Central Asia. However, evolutionary and genetic research on L. capensis was seriously impeded by the absence of a reference genome. Here, we assembled and constructed a chromosome-level genome of L. capensis (with scaffolds anchored to 25 chromosomes and a total assembled length of 2.9 Gb, achieving a contig N50 length of 124.44 Mb) using PacBio HiFi sequencing and Hi-C assembly technology. Evaluation using BUSCO indicated the genome assembly to be 98.2% complete. The de novo prediction revealed that repetitive sequences constitute 46.13% of the entire genome, and long interspersed nuclear elements (LINEs) constituted the largest portion. We annotated a total of 13, 868 protein-coding genes using transcriptomes from two tissues (muscle and skin). This high-quality reference genome serves as a valuable genomic resource for advancing genetic studies in this species. [ABSTRACT FROM AUTHOR]

Large fruit size is one of the most important breeding objectives for sweet cherry. In the Washington State University (WSU) breeding program, large-fruited germplasm exists, and heritability is reasonably high. An important genetic locus for cherry fruit size has been identified but appears to primarily distinguish between wild and improved phenotypes and may have limited utility in the breeding program. We employed association mapping and genomic prediction approaches to identify markers and models for fruit size in germplasm relevant to the breeding program. The germplasm consisted of 247 individuals from two sub-populations. The "RosBREED" sub-population (n = 106) was genotyped with the cherry 6 K Illumina SNP array. The "program" sub-population (n = 141) was genotyped with the cherry 6 + 9 K SNP array. Each sub-population was phenotyped for fruit diameter for two seasons. Sub-populations were analyzed individually as well as combined. SNPs for the combined dataset included those common to both arrays. Significantly associated SNP markers for fruit diameter were identified on all 8 chromosomes using BLINK. Individual markers accounted for up to 33% of phenotypic variance. In all but two cases, the minor allele was associated with smaller fruit. However, minor allele frequencies were 0.25–0.44 for four significant SNPs, indicating the opportunity for continued selection. Seven markers were converted to locus-specific assays for validation and use in marker-assisted selection and showed a concordance rate ≥ 97.6%. Genomic prediction models were developed using BGLR. Selection accuracy ranged from 0.38 to 0.53 depending on the population and year. These results indicate that either association mapping or genomic prediction can be used to select for larger fruit in sweet cherry, although genomic prediction might be more efficient in improved germplasm if a cost-effective genotyping platform is available. [ABSTRACT FROM AUTHOR]

The cultivated apple (Malus domestica Borkh.) is an economically important fruit crop in countries worldwide, including Bosnia and Herzegovina (BIH).The gene bank activities in BIH were initiated in the 1930s and continued until the war in the 1990s, when much of the documentation was lost. Since then, uncoordinated efforts were made to establish apple collections in different regions, but a comprehensive analysis of genetic resources was lacking. This prompted the current study where we present the first thorough overview of the national genetic resources of BIH apples. Thus, we analyzed 165 accessions in the apple gene bank at the Institute for Genetic Resources (IGR) established at Banja Luka using the 20 K apple Infinium® single nucleotide polymorphism (SNP) array. We combined the results with previously published data on the germplasm collections at Srebrenik and Goražde, genotyped using the Axiom® Apple 480 K SNP array. In total, 234 accessions were included in the study of which 220 were presumed to be local cultivars and 14 were known international reference cultivars. We identified numerous genotypic duplicates within and between collections and suggested preferred names to be used in the future. We found the BIH germplasm to have relatively few parent-offspring relationships, particularly among local cultivars, which might reflect the country's history and patterns of apple cultivar introduction. A number of cultivars unique to BIH and a weakly defined genetic group were identified via STRUCTURE analysis, representing interesting targets for future research and preservation efforts. [ABSTRACT FROM AUTHOR]

Despite extensive introductions of Eucalyptus germplasm to Brazil in the last 50 years, relatively little is known about the genetic diversity within current breeding programs, particularly for non-mainstream species. A prime example is Eucalyptus benthamii, a subtropical species with a restricted natural range, endangered due to anthropogenic population fragmentation. We used microsatellite markers to reconstruct the pedigrees and estimate diversity within the two most representative pools of E. benthamii germplasm managed in separate, commercial Brazilian breeding populations. The analysis, together with evidence from Australian Tree Seed Centre (ATSC), historical germplasm export data confirmed that the genetic diversity within the two populations is modest. In the two breeding populations, the estimated status number was in the range of 8.5–22.0 per population considering marker-based co-ancestry. Extensive close relatedness and family structure were identified within and across the two populations, confirming that they share a high proportion of founder ancestors. This is likely a result of the narrow genetic base of the initial introductions and subsequent directional selection and breeding. With the increasing importance of E. benthamii in Brazilian plantation forestry, and as further breeding will likely reduce the status number, our study highlights the need for infusions to augment the existing genetic diversity. Complementary to sourcing infusions, implementing breeding strategies that take advantage of the marker-based information reported in this study to carefully manage the pedigree should help to minimise inbreeding. Exchanging unrelated individuals between the two Brazilian breeding populations would also be advantageous. [ABSTRACT FROM AUTHOR]

Eastern black walnut, Juglans nigra L., is an economically important tree species valued for its high-quality timber and edible nuts. A regional industry for the species' nut and kernel products resides in Missouri, where over 9 million kg of hulled in-shell nuts are purchased in masting years. The crop is primarily based upon nuts harvested from wild trees, placing a ceiling on nut volume and quality (e.g. small nut size, dark pellicle color, and 10–14% kernel by weight). Orchards of named cultivars, like 'Kwik Krop' and 'Sparrow', supply up to 22,000 kg of nuts with a higher kernel percentage (> 26%) and improved quality. Such cultivars often represent chance wild or on-farm seedlings, clonally propagated since the late 1800's by enthusiasts. Today, continued improvement of eastern black walnut as an orchard crop is limited by a long generation time, delayed expression of important traits, and space requirements – creating a strong need for marker-trait association studies that inform progeny selection. The first linkage map for J. nigra was recently created using the 'Sparrow' × 'Schessler' F1 population and loci for phenology traits discovered. The objective of this study is to utilize these genetic resources to detect quantitative trait loci (QTL) and report associated DNA markers for the spur-bearing habit, which promotes precocity and high yield. Using single-year data from the 11-year-old population, we observe that segregation for the spur-bearing habit appears to be recessive and multigenic. Three QTLs (p > 0.99) were identified on linkage group (LG) 8, LG11, and LG16 that explain 7.2%, 8.7%, and 10% of trait variation, respectively. Regions between flanking DNA markers were 3.16 cM, 4.32 cM, and 9.69 cM, respectively. This study is the first to examine the genetic control of bearing habit and yield in eastern black walnut and informs breeders' approach for their future genetic improvement. [ABSTRACT FROM AUTHOR]

Analysis and dissection of native germplasm resources and characterization of their relationships are essential for conservation and plant breeding programs. To study the diversity pattern of alfalfa populations in the East Azerbaijan province of Iran, 900 accessions belonging to 30 local populations were collected and subjected to microsatellite profiling. Seven simple sequence repeat (SSR) loci were harnessed to analyze and characterize the studied populations. Data driven from microsatellite markers were analyzed, and diversity indices such as the effective number of alleles, polymorphic information content (PIC), and Shannon's index underwent estimation. Moreover, cluster analysis using the neighbor-joining algorithm and principal coordinate analysis were further performed to elucidate the relationships among the studied populations. Totally, 47 SSR alleles were observed in the studied alfalfa populations. The mean allele numbers per locus were 6.71 and ranged from 2 to 12. Additionally, the PIC for the applied SSRs was 0.66. The analysis of molecular variance indicated a significant difference between and within the studied alfalfa populations (P < 0.00001). Furthermore, genetic distance analysis demonstrated that populations are clustered into three distinct groups, of which Ghara-Yonjeh had a larger distance from other populations. These results revealed that the studied local population in the northwest regions of Iran harbors higher genetic diversity and is a valuable resource for future alfalfa germplasm conservation and breeding programs. [ABSTRACT FROM AUTHOR]

Knowledge of genetic diversity is one of the most essential tasks for sustainable management of medicinal plants. In the present study, the molecular variability and population structure in a set of Ferula assafoetida accessions collected from different geographical regions of Iran were evaluated using start codon targeted polymorphism (SCoT) and universal rice primer (URP) markers. Based on results, SCoT (12 primers) and URP (12 primers) markers amplified 192 and 149 polymorphic fragments, respectively. The polymorphism information content (PIC) estimated by URP and SCoT ranged from 0.31 to 0.43, and 0.34 to 0.44, respectively. The analysis of molecular variance revealed the greater genetic variation within population compared to among them. The Kerman's population showed the highest values for the heterozygosity (He), percentage of polymorphic bands (PPB), Shannon's information index (I), and effective number of alleles (Ne). The neighbor joining (NJ) clustering algorithm grouped all investigated accessions into six and five main groups based on URP and SCoT data, respectively. The results of structure analysis based on both marker systems showed that all accessions were divided into five subpopulations. Furthermore, principal coordinate analysis (PCoA) supported these findings. In conclusion, our results revealed a high level of genetic diversity and gene flow between F. assafoetida populations. Moreover, the SCoT markers were more effective than URP in detecting the genetic diversity in F. assafoetida populations. Hence, the use of SCoT markers in further genetic research such as genetic fingerprinting and association analysis would be recommended. [ABSTRACT FROM AUTHOR]

Identifying and selecting superior genotypes in different countries and regions is a valuable breeding method in walnuts. The present study evaluated 31 quantitative and qualitative traits of seven superior walnut genotypes comparable to 'Jamal', 'Lara', and 'Serr' cultivars. The comparisons followed IPGRI descriptions. We evaluated pomological traits in the superior genotypes for four consecutive years (2019, 2020, 2021, and 2022), observing high variations among the genotypes. The thickness of husk, fruit weight, nut weight, and nut length ranged between 2.47–4.08 mm, 42.26–58.38 g, 10.43–14.60 g, and 29.59–37.61 mm, respectively. Also, kernel weight, percentage, color, plumpness, and fillness ranged between 5.22–6.97 g, 40.18–54.75%, 1.33–2.67 (approximately light), 2.33 (medium)—3.00 (plump), and 4.78 (medium)—7.00 (good), respectively. Biochemical features in the kernels varied significantly among the genotypes, particularly in the case of oil content (62.26–70.08%), SFA (10.10–13.03%), MUFA (13.38–36.40%), and PUFA (52.05–74.40%). Furthermore, kernel protein content, total polyphenols, and antioxidant activity ranged between 16.79–21.61%, 58.78–95.06 mg GAE/g, and 0.15–0.22 EC50, respectively. The kernel percentage correlated significantly and negatively with the flowering type (r = −0.414) and nut weight (r = −0.467) but positively with DFO (r = 0.545), fruitfulness percentage (r = 0.471), kernel weight (r = 0.412), saturated fatty acid (r = 0.375), oil percentage (r = 0.472), and protein percentage (r = 0.422). These genotypes were superior due to closed-shell seal, light kernel color, ease of kernel removal from nuts, lateral bearing, high kernel percentage, and high nutritional value. The selected genotypes are the bearers of desirable genes for future walnut breeding programs. [ABSTRACT FROM AUTHOR]

Avocado (Persea americana Mill.) is a fruit tree species that grows in different regions of the world. The edible fruit and other parts of the avocado tree have immense nutritional, oil-bearing, and medicinal value. The plant is native to Guatemala but was introduced to Ethiopia by missionaries in 1939. In southern Ethiopia, where coffee is the main cash crop, it is used as a shade for plants. However, in the past 25 years, many farmers and urban dwellers have begun to use avocados as a valuable source of income. Hence, there is a need for quality avocado trees for commercial purposes. Although there is conjecture about the wide variation in avocados in Ethiopia, the diversity and population structure of this plant has not been described. This study aims to fill this gap by comparing avocado germplasm from Guatemala and Ethiopia. A sample of 298 avocados was collected from three and four populations in Guatemala and Ethiopia, respectively. Population diversity and structure were assessed using 12 simple sequence repeat (SSR) markers. The SSR marker profile detected 112 alleles, with an average of 10.21 per locus and an average PIC value of 0.84. Genetic diversity was high, with an average of 10.2 alleles per locus, a mean Shannon index value of 1.65, and observed and expected heterozygosity of 0.51 and 0.71, respectively. The expected heterozygosity varied between populations and was highest in West Guatemala (0.85) and lowest in Gamo (0.55). An analysis of molecular variance showed that 18% of the genetic variation was between the continents and only 2% among the populations. The pairwise genetic differentiation coefficient ( F ST ) indicated high differentiation between populations. The phylogenetic tree, structure, discriminant analysis of the main components, and Nei's genetic distance analysis confirmed three groups of avocados. The Wondo Genet population was more genetically diverse than the populations from the Sidama, Wolaita, and Gamo regions. Furthermore, it revealed little genetic exchange with these populations, unlike the Guatemalan avocado, indicating the presence of unique alleles among avocados in Ethiopia. The landraces from Sidama, Wolaita, and Gamo appeared to have experienced historical drift events. [ABSTRACT FROM AUTHOR]

Siberian wildrye (Elymus sibiricus) is a xero-mesophytic forage grass with high nutritional quality and stress tolerance. Among its numerous germplasm resources, some possess superior drought resistance. In this study, we firstly investigated the physiological differences between the leaves of drought-tolerant (DT) and drought-sensitive (DS) genotypes under different field water contents (FWC) in soil culture. The results showed that, under drought stress, DT maintained a lower leaf water potential for water absorption, sustained higher photosynthetic efficiency, and reduced oxidative damage in leaves by efficiently maintaining the ascorbic acid-glutathione (ASA-GSH) cycle to scavenge reactive oxygen species (ROS) compared to DS. Secondly, using RNA sequencing (RNA-seq), we analyzed the gene expression profiles of DT and DS leaves under osmotic stress of hydroponics induced by PEG-6000. Through differential analysis, we identified 1226 candidate unigenes, from which we subsequently screened out 115/212 differentially expressed genes (DEGs) that were more quickly induced/reduced in DT than in DS under osmotic stress. Among them, Unigene0005863 (EsSnRK2), Unigene0053902 (EsLRK10) and Unigene0031985 (EsCIPK5) may be involved in stomatal closure induced by abscisic acid (ABA) signaling pathway. Unigene0047636 (EsCER1) may positively regulates the synthesis of very-long-chain (VLC) alkanes in cuticular wax biosynthesis, influencing plant responses to abiotic stresses. Finally, the contents of wax and cutin were measured by GC–MS under osmotic stress of hydroponics induced by PEG-6000. Corresponding to RNA-seq, contents of wax monomers, especially alkanes and alcohols, showed significant induction by osmotic stress in DT but not in DS. It is suggested that limiting stomatal and cuticle transpiration under drought stress to maintain higher photosynthetic efficiency and water use efficiency (WUE) is one of the critical mechanisms that confer stronger drought resistance to DT. This study provides some insights into the molecular mechanisms underlying drought tolerance in E. sibiricus. The identified genes may provide a foundation for the selection and breeding of drought-tolerant crops. [ABSTRACT FROM AUTHOR]

Rice grain size and grain weight, which have a great influence on rice quality and yield, are complex quantitative traits that are mediated by grain length (GL), grain width (GW), length-to-width ratio (LWR), and grain thickness (GT). In this study, the BC1F2 and BC1F2:3 populations derived from a cross between two indica rice varieties, Guangzhan 63-4S (GZ63-4S) and Dodda, were used to locate quantitative trait loci (QTL) related to grain size. A total of 30 QTL associated with GL, GW and LWR were detected, of which six QTL were scanned repeatedly in both populations. Two QTL, qGL4 and qGL6, were selected for genetic effect validation and were subsequently fine mapped to 2.359 kb and 176 kb, respectively. LOC_Os04g52240 (known as OsKS2/OsKSL2), which encoding an ent-beyerene synthase and as the only gene found in 2.359 kb interval, was proposed to be the candidate for qGL4. Moreover, the grains of qGL4 homozygous mutant plants generated by the CRISPR-Cas9 system became shorter and wider. In addition, the qGL4 allele from GZ63-4S contributes to the increase of yield per plant. Our study not only laid the foundation for further functional study of qGL4 and map-based cloning of qGL6, but also provided genetic resources for the development of high yield and good quality rice varieties. [ABSTRACT FROM AUTHOR]

Tiller angle (TA) is one of the most important agronomic traits that directly affects plant architecture, photosynthetic efficiency, and planting density of rice. Although many quantitative trait loci (QTLs) and associated genes for TA have been identified, the detection of TA QTLs still needs attention. This study used 238 micro-core germplasm populations for genome-wide association analysis (GWAS) of the TA. The frequency distribution of TA presented continuity in 2018 and 2019, with five QTLs designated as qTA1, qTA2, qTA6, qTA9, and qTA12. These QTLs explained phenotypic variation ranging from 5.94 to 12.38%. Among them, qTA2 and qTA6 were new QTLs of TA, and only qTA1 was detected repeatedly in 2 years. Then, 253 germplasm from the 3K Rice Genome Project were used for candidate gene and haplotypes analysis; the results showed that LOC_Os01g67770, LOC_Os02g35180, and LOC_Os09g38130 were the candidate genes of qTA1, qTA2, and qTA9, respectively. These results provided insight into the genetic improvement of plant architecture in rice. [ABSTRACT FROM AUTHOR]

Rice, a staple crop that feeds more than one-third of the world's population, encounters a wide range of biotic and abiotic stresses due to climate change. Rising temperature is one of the significant abiotic stresses affecting rice productivity worldwide. The development of heat-tolerant rice cultivars is critical in this regard. Weedy rice could potentially serve as a natural resource for genes conferring agronomically important traits beneficial to cultivated rice. However, heat tolerance in both cultivated and weedy rice is still understudied. This study screened a set of 180 weedy rice accessions for heat stress tolerance and further characterised them using genome-wide single-nucleotide polymorphisms (SNPs) analysis. Five heat-tolerant (HT) accessions (MU244, MU235, MU249, MU260 and MU237), along with five heat-susceptible (HS) accessions (MU100, MU114, MU264, MU251 and MU005), were subjected to relative electrical conductivity (REC) test and reactive oxidative species assay (ROS). These tests verified that the five HT accessions performed better under heat stress than their HS counterparts. In addition, whole-genome sequences of three HT (MU235, MU237 and MU066) and four HS (MU100, MU114, MU022 and MU005) accessions were selected for the genome-wide SNPs comparison, revealing substantial amino acid variation in the heat-tolerance-related genes between the HT and HS rice groups. The proposed genes and genome-wide SNP markers may help rice breeders better understand how different rice cultivars respond to heat stress. [ABSTRACT FROM AUTHOR]

Drought is a major constraint for maize production in sub-Saharan Africa. Developing high-yielding drought-tolerant maize germplasm will safeguard maize yields in the ever-increasing fluctuating rainfall conditions. This study aimed to identify high-yielding inbred lines with stable performance for utilization in hybrid production. One hundred eighty-two (182) maize inbred lines were evaluated under well-watered and drought-stressed conditions at Ukulinga, Makhathini, and Cedara research stations in KwaZulu-Natal, South Africa. The experiments were carried out in a 13 × 14 alpha lattice design with two replications. The inbred lines exhibited significant differences (p ≤ 0.001) for grain yield and yield-related traits under well-watered and drought-stressed environments. The GGE biplot identified three mega-environments, clearly separating drought-stressed from well-watered environments. Inbred lines TZISTR1190, TZISTR1231, TZISTR1261 and CML540 were superior under well-watered conditions, while TZISTR1164 and CML390 performed well under drought condition. TZISTR1190 displayed both high average yield and stability across environments. Inbred lines combining stable high yielding performance in optimum and stress conditions such as TZISTR1190 and TZISTR1231, can be incorporated into local maize breeding pipelines to develop stable high yielding resilient hybrids. [ABSTRACT FROM AUTHOR]

The identification of genotypes with high yield and yield stability under drought is the first step towards the generation of novel lines with better adaptation to climate change variation. The aim of this work was to explore the efficiency of ten different drought tolerance indices to identify superior genotypes. Ten wheat genotypes were evaluated for two years under two irrigation regimes: control and water deficit. As expected, the water deficit reduced the phenotypic values, of the evaluated traits in tested wheat cultivars. Significant positive correlations were found considering the grain-yield under both regimes (Yp, Ys), and three drought tolerance indices (DTIs): the Mean Productivity Index (MP), the Stress Tolerance Index (STI) and the Geometric Mean Productivity (GMP). These correlations were confirmed in Bi-plot analysis and the graphical separation of tested genotypes associated with different performances in drought indices. MP, STI and GMP indices consistently selected BioInta 2002, Baguette 9 and BioInta 2004 as the drought tolerant materials, and conversely, Baguette P. 11, BioInta 1005 and Pampeano as drought susceptible materials. These analyses positionate MP, STI and GMP as appropriate tools to find genotypes with contrasting drought response to drought to later be incorporated as genetic resources into breeding programs. [ABSTRACT FROM AUTHOR]

Penaeus monodon is a crucial economic crustacean globally and a focal point of aquatic research. Germplasm resources provide a diverse food source for humans, meeting various nutritional needs; they also maintain plant and animal gene banks, enhancing resilience, adaptability, and promoting ecological balance in terms of genetic diversity. To accurately assess the germplasm resources of P. monodon, we conducted a comprehensive investigation. We analyzed muscle characteristics, nutrient content, amino acids, fatty acids, and genetic diversity using whole-genome sequencing in six P. monodon groups. The results showed that the crude protein content of the six groups of P. monodon was 21.17–24.60 g/100 g, crude fat content was 0.60–0.80 g/100 g, essential amino acid content was 5.44–6.41 g/100 g, total amino acid content was 15.68–18.63 g/100 g, and total fatty acid content was 354.78–587.43 mg/100 g. Genetic differentiation index (Fst) values ranged from 0.029 to 0.604 for six groups. PmSZ has a good genetic condition. There was no significant difference in crude fat in conventional nutrients, and the difference in biochemical indexes T-AOC, CAT, and SOD was not significant (P > 0.05). The noteworthy point is that the analysis of genetic diversity reveals a moderate level of genetic diversity. PmDF and PmZH exhibit the highest degree of differentiation, while PmRP and PmZH show the lowest degree of differentiation. Our survey results establish a critical foundation for comprehending and harnessing the germplasm resources essential for selectively breeding robust P. monodon populations. [ABSTRACT FROM AUTHOR]

This study elucidates to generate a linkage map for Portuguese oysters, Crassostrea angulata, and recognise potential markers linked to economical traits in C. angulata. Genome-wide association studies (GWAS) using 19,475 single nucleotide polymorphisms (SNPs) generated by a genotyping-by-sequencing approach consisting of 647 individuals in two selection generations of C. angulata, consisting of 57 full-sib family of the first generation and 33 full-sib family of the second generation. GWAS identified six significant SNPs linked to whole weight (P < 10−4). These six SNPs explained 10.2% of the total genetic variance of whole weight. Additionally, three SNPs were identified linked to meat yield (i.e., soft tissue weight) and contributed to 9.2% of the total genetic variance for this trait. By linkage analysis on the raw data, a total of 19,475 SNP markers were mapped to 10 linkage groups, with an average density of 19.1 SNPs per cM. This linkage map was developed and potential markers identified for whole weight and soft tissue weight provide a novel resource to characterise the genetic structure of economic traits in C. angulata. [ABSTRACT FROM AUTHOR]

The symptoms caused by viroids differ, ranging from asymptomatic to mild-or-severe symptoms. Pepper plant symptoms caused by the Pepper chat fruit viroid (PCFVd) are mild compared to those affecting tomato plants; however, there is not much more known of the symptomatology on pepper plants. Symptoms that could be used for disease virulence assessment in pepper plants were elucidated from 31 commercial pepper cultivars belonging to Capsicum annuum and C. frutescens that had been purchased from agricultural shops. The plants were mechanically sap-inoculated at the seedling growth stage and observed weekly for symptom development, with disease virulence evaluations performed at 4, 8, and 12 weeks post inoculation. Infection of all plants was verified based on reverse transcription-polymerase chain reaction, along with visual evidence of growth reduction, including leaf rugosity and leaf size reduction, a narrow canopy of the blocky and elongated fruit shapes for C. annuum and explicit apical stunting with small apical leaves of the elongated fruit type for C. frutescens. The disease virulence assessment was designed based on these symptoms to produce a score with 0–10 disease virulence levels (DVLs). The results showed that the pepper cultivars displayed responses to PCFVd with DVL scores of 1.00–8.00, with no PCFVd transmission being recorded from seeds to seedlings for the 3 test cultivars. This finding indicated that the genetic resources of pepper cultivars against PCFVd were as low as 1.00 DVL. However, the low DVL pepper cultivars could provide an inoculum source to other susceptible plants via mechanical transmission. [ABSTRACT FROM AUTHOR]

Priming is a phenomenon that has received special interest in recent years to better understand plant acclimation to environmental cues and its potential use in improving the drought response in susceptible crops. Crop wild relatives (CWR) play a role in natural ecosystems, are part of agrobiodiversity, and represent essential genetic resources for crop breeding. Although priming to drought has been demonstrated in the cultivated potato (Solanum tuberosum), it has been overlooked in potato CWR. Solanum kurtzianum is an Argentinian wild potato species adapted to arid conditions and represents a promissory model to study drought memory. The aim of the study was to evaluate the priming effect in two genotypes of S. kurtzianum of contrasting drought tolerance (G1 and G2). We obtained plants from tubers of a previous experiment, where plants were subjected to well-watered (non-primed) and moderate water-deficit (primed) conditions. Primed and non-primed plants were then grown under three irrigation treatments: i) well watered (WW), ii) moderate water deficit (MWD), and iii) severe water deficit (SWD). Morphological, physiological, biochemical, and yield traits were evaluated. Both genotypes presented higher biomass when they were exposed to a previous water deficit. G1 primed plants showed major above-ground biomass in MWD, whereas G2 primed plants showed major stolon biomass in SWD. According to drought tolerance indices, primed plants were more tolerant to water deficit than the non-primed ones. These results suggest that there are different priming effects to drought that would favour sexual or asexual modes of reproduction in the Andean desert potato S. kurtzianum. [ABSTRACT FROM AUTHOR]

Online Mendelian Inheritance in Animals (OMIA) is a freely available curated knowledgebase that contains information and facilitates research on inherited traits and diseases in animals. For the past 29 years, OMIA has been used by animal geneticists, breeders, and veterinarians worldwide as a definitive source of information. Recent increases in curation capacity and funding for software engineering support have resulted in software upgrades and commencement of several initiatives, which include the enhancement of variant information and links to human data resources, and the introduction of ontology-based breed information and categories. We provide an overview of current information and recent enhancements to OMIA and discuss how we are expanding the integration of OMIA into other resources and databases via the use of ontologies and the adaptation of tools used in human genetics. [ABSTRACT FROM AUTHOR]

Exposing genetic material with physical mutagens can create novel genetic resources capable of combating different stresses. High throughput GBS-DArTseq™ assay was deployed to estimate genetic diversity of 33 newly developed stable wheat mutants as compared to the wild type. The identified 1,57,608 PAVs markers were randomly distributed across wheat chromosomes and sub-genomes with the highest number detected on Chr-7D (2877) and Chr-7B (2711). The B sub-genome contained the most PAVs followed by D and A-sub genome. Among mutant lines, Pb-M-2061 and Pb-M-59 had the highest PAV count, while Pb-M-605 and Pb-M-196 had the lowest. A total of 7,910 PAVs were consistently present over all replicates, with 3,252 specifically present in mutants and absent in wild type. The maximum PAVs (1480) were found in Pb-M-1027 and Pb-M-1323 (656). Functional characterization revealed that out of 3,252, 1,238 were found in wheat transcriptome database that contained 152 characterized and 1,196 uncharacterized genes. COGs and GO-terms analysis linked many PAVs with pathways involving signaling, metabolism and defense. Maximum number of gene-containing PAVs were identified in Pb-M-1027, Pb-M-2302 and Pb-M-1323 which were involved in tolerance to diseases and abiotic stresses, improved photosynthetic efficiency, larger grain size, increased grain yield and harvest index pathways. This study provides valuable insights into the genetic diversity and potential agronomic benefits of PAVs in wheat mutant lines. These findings can help molecular geneticist and breeders for exploiting the induced genetic diversity for unravelling the genetic circuits as well as exploiting in wheat breeding for developing resilient cultivars. [ABSTRACT FROM AUTHOR]

Cryopreservation of receptacles or fertilized eggs is the main method for the preservation of indoor germplasm resources for the economic seaweed Sargassum fusiforme. However, none of these methods can achieve long-term preservation of germplasm resources. The holdfast represents the asexual reproductive organ of S. fusiforme and has a dense tissue that can be regenerated into seedlings under suitable conditions. Therefore, in this study, the holdfast was used as the experimental material to analyze the effects of different temperatures (8 °C, 10 °C, 13 °C) and salinities (29‰, 24‰, 19‰, 14‰) on the preservation of S. fusiforme germplasm. The results showed that 29‰ and 14‰ were not suitable for the long-term preservation of holdfasts regardless of temperatures, since both photosynthesis and growth rates of the holdfast decreased after 30 days of preservation at these salinities. However, 8 °C and 19‰ were found to be suitable for the long-term in vitro preservation of holdfasts, with a survival time being as long as 120 days. During the experiment, the photosynthesis activity of the holdfast also displayed less fluctuation in this experimental condition than in the others. After 120 days, the content of malondialdehyde in the holdfasts was the lowest, and the morphology remained intact. 8 °C and 19‰ could be suitable for long-term indoor preservation of S. fusiforme. These findings might provide technical support for solving the problem associated with the difficulty of preserving the germplasm of superior strains in the breeding process. They might also have important significance for crossbreeding and for establishing a germplasm resource bank for S. fusiforme in the future. [ABSTRACT FROM AUTHOR]

The current endeavor aims to explore the regeneration capabilities of Nyctanthes arbor-tristis (Harsinghar), a medicinal plant, through shoot stem explants. This research is crucial, for both conservation of the plant and harnessing its properties. Fresh shoot stem explants were precisely procured and cultivated onto Murashige and Skoog (MS) medium, containing diverse concentrations of plant growth regulators like benzyl adenine (BA) or kinetin (KIN) at 0.5, 1.0, 2.5, 5.0, 7.5 and 10.0 µM and indole-3-butyric acid (IBA), indole-3-acetic acid (IAA) or α-napthalene acetic acid (NAA) at 0.1, 0.5, and 1.0 µM concentrations. MS medium supplemented with 2.5 µM Kinetin and 0.5 µM NAA blend, proved to be the best combination for achieving a higher rate (90%) of shoot multiplication (20.33). Rhizogenesis was achieved best via ex vitro rooting method using 200 µM IBA for 30 min forming 6.33 roots. Regenerated plants were also examined for antioxidant enzymatic activities and photosynthetic pigments to assess their ability to cope with the external environmental conditions during acclimatization. As compared from first day of ex vitro transfer of regenerated plants, the higher content of photosynthetic pigments contents and fluctuations in levels of antioxidant enzymes [superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR)] activities during the course of acclimatization, indicates a better adaptive and resilient behavior to the external stressed environmental conditions. Beyond mere multiplication, this methodology sets the stage for comprehensive investigations into the pharmacological research and genetic enhancements of N. arbor-tristis, enriching its rank in the realm of sustainable botanical resources. Key message: The study develops an in vitro regeneration approach for conserving, adapting and utilizing N. arbor-tristis, by optimizing plant growth regulators regime, physiological and antioxidant enzymatic activities. [ABSTRACT FROM AUTHOR]

The giant river prawn (Macrobrachium rosenbergii) is one of the most widely cultured crustacean species. In recent years, its aquaculture has faced challenges, including the degradation of germplasm resources and the emergence of viral diseases. Genomic information can be a valuable resource for developing molecular breeding programs for this important aquaculture species. Here we constructed a high-quality reference genome for M. rosenbergii by integrating Nanopore, Illumina, and high-throughput chromosome conformation capture (Hi-C) technologies. The final genome assembly is 3.18 Gb in size, with scaffold N50 and contig N50 of 62.73 Mb and 8.92 Mb, respectively. Approximately 98.6% of the assembled sequences were anchored into 59 pseudo-chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of the genome assembly reached 94.5%. Repetitive sequences comprise 43.77% of the assembled genome, and 17,436 protein-coding genes were annotated. The high-quality genome of M. rosenbergii will empower molecular breeding efforts and provide invaluable resources for comparative genomic analysis of decapod species. [ABSTRACT FROM AUTHOR]

Spinibarbus caldwelli is an important freshwater economic fish in China. Owing to uncontrolled fishing, wild resources of S. caldwelli have decreased rapidly and may be on the verge of extinction. In this study, utilizing single-molecule real-time (SMRT) sequencing technology and chromatin interaction mapping (Hi-C) technologies, we assembled the first chromosome-scale genome for S. caldwelli about 1.77 Gb in size, with a contig N50 length of 11.83 Mb and scaffold N50 length of 33.91 Mb. In total 1.72 Gb (97.01%) of the contig sequences were anchored onto fifty chromosomes with the longest scaffold being 56.20 Mb. Furthermore, proximately 49.41% of the genome was composed of repetitive elements. In total, 49,377 protein-coding genes were predicted, of which 47,724 (96.65%) genes have been functionally annotated. The high-quality chromosome-level reference genome and annotation are vital for supporting basic genetic studies and will be contribute to genetic structure, functional elucidation, evolutionary inquiry, and germplasm conservation for S. caldwelli. [ABSTRACT FROM AUTHOR]