Key Breeding Research Articles

Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets.

Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.

Development and Identification of a Wheat-Rye Breeding Line for Harmonious Improvement Between Powdery Mildew Resistance and High Yield Potential.

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is a devastating disease that seriously threatens wheat yield and quality. To control this disease, host resistance is the preferred measure. However, wheat breeding is a complex process with elusive exchange and recombination of the traits from their parents. Increased resistance often leads to a decline in other key traits, such as yield and quality. Developing breakthrough germplasms with harmonious powdery mildew resistance and other key breeding traits is attractive in wheat breeding. In this study, we developed an ideal wheat breeding line AL46 that pyramided its hexaploid triticale parent-derived desirable yield traits and its wheat parent-derived powdery mildew resistance gene Pm2. Sequential genomic in situ hybridization (GISH), multicolor GISH, multicolor fluorescence in situ hybridization, and molecular marker analyses revealed that AL46 was a wheat-rye T1RS·1BL translocation line. Genetic analysis combined with function marker detection and sequence alignment were used to confirm that AL46 carried the Pm2 gene. Then, we evaluated the powdery mildew resistance and comprehensive traits of AL46, and just as we designed, AL46 showed harmonious powdery mildew resistance with some key breeding traits. This study not only developed an ideal wheat germplasm resource but also provided a successful example for pyramiding breeding, which could be a promising direction for wheat improvement in the future.

Efficacy of household Aedes larval control practices in a peri-urban township, Yangon, Myanmar: Implication for entomological surveillance

Dengue is a major public health concern in Myanmar. We carried out a cross-sectional study to investigate the efficacy of larval control practices in household water containers, such as the use of the larvicide, temephos, covering the containers with lids and weekly cleaning. We surveyed 300 households in Kaw Hmu Township, a peri-urban community in the Yangon region. We inspected 1,892 water storage containers and 342 non-water storage/household waste containers during the rainy season and 1,866 water storage containers and 287 non-water storage/household waste containers during the dry season. The presence of Aedes larvae and larval control measures were recorded for each container. Results revealed that larval indices were higher than World Health Organization standard indices, and infestations in water storage containers were more common in the rainy season (6.6%) than in the dry season (5.7%). Infestations were also more likely in containers of non-potable water (9.1%–9.9%) than in containers of potable water (0.1%–0.7%). Two thirds of water storage containers were treated with temephos. Containers most likely to contain Aedes larvae were cement basins and barrels. Temephos was effective in controlling infestations in cement basins, while weekly cleaning was effective in controlling infestations in barrels. Combinations of control methods were more effective at larval control than the use of a single method. Larval infestations were high (18.4% in the rainy season) in unused containers and in containers which were household waste. Overall, we found a complex interaction between household water use, container characteristics, and larval control practices. Larval control strategies in Myanmar will require ongoing entomological surveillance and the identification of key breeding sources and optimal control methods.

Gray whale detection in satellite imagery using deep learning

AbstractThe combination of very high resolution (VHR) satellite remote sensing imagery and deep learning via convolutional neural networks provides opportunities to improve global whale population surveys through increasing efficiency and spatial coverage. Many whale species are recovering from commercial whaling and face multiple anthropogenic threats. Regular, accurate population surveys are therefore of high importance for conservation efforts. In this study, a state‐of‐the‐art object detection model (YOLOv5) was trained to detect gray whales (Eschrichtius robustus) in VHR satellite images, using training data derived from satellite images spanning different sea states in a key breeding habitat, as well as aerial imagery collected by unoccupied aircraft systems. Varying combinations of aerial and satellite imagery were incorporated into the training set. Mean average precision, whale precision, and recall ranged from 0.823 to 0.922, 0.800 to 0.939, and 0.843 to 0.889, respectively, across eight experiments. The results imply that including aerial imagery in the training data did not substantially impact model performance, and therefore, expansion of representative satellite datasets should be prioritized. The accuracy of the results on real‐world data, along with short training times, indicates the potential of using this method to automate whale detection for population surveys.

A method for partitioning trends in genetic mean and variance to understand breeding practices

BackgroundIn breeding programmes, the observed genetic change is a sum of the contributions of different selection paths represented by groups of individuals. Quantifying these sources of genetic change is essential for identifying the key breeding actions and optimizing breeding programmes. However, it is difficult to disentangle the contribution of individual paths due to the inherent complexity of breeding programmes. Here we extend the previously developed method for partitioning genetic mean by paths of selection to work both with the mean and variance of breeding values.MethodsFirst, we extended the partitioning method to quantify the contribution of different paths to genetic variance assuming that the breeding values are known. Second, we combined the partitioning method with the Markov Chain Monte Carlo approach to draw samples from the posterior distribution of breeding values and use these samples for computing the point and interval estimates of partitions for the genetic mean and variance. We implemented the method in the R package AlphaPart. We demonstrated the method with a simulated cattle breeding programme.ResultsWe show how to quantify the contribution of different groups of individuals to genetic mean and variance and that the contributions of different selection paths to genetic variance are not necessarily independent. Finally, we observed that the partitioning method under the pedigree-based model has some limitations, which suggests the need for a genomic extension.ConclusionsWe presented a partitioning method to quantify sources of change in genetic mean and variance in breeding programmes. The method can help breeders and researchers understand the dynamics in genetic mean and variance in a breeding programme. The developed method for partitioning genetic mean and variance is a powerful method for understanding how different selection paths interact within a breeding programme and how they can be optimised.

Population Status of the Globally Threatened Long-Tailed Duck Clangula hyemalis in the Northeast European Tundra

Arctic Russia is home to more than 90% of all Long-tailed Ducks in the Clangula hyemalis species from the Western Siberia/Northern Europe population. The breeding population in European Russia was estimated to be about 5 million birds in the 1960s, while today, estimates have declined to 1 million birds. Up until now, the main reasons for the overall population decline of the Long-tailed Duck were related to wintering conditions in the Baltic Sea. Our data indicate that the loss or deterioration of key breeding habitats in the Arctic regions of Russia is one important factor influencing the rapid population decline. Many key breeding habitats of the Long-tailed Duck were completely lost in the Bolshezemelskaya tundra, as this area was transformed into major oil and gas extraction sites. The transformation of these sites increased the disturbance and oil pollution of adjacent habitats, leading to the direct loss of certain key nesting sites and a marked and rapid decline of the breeding population of the Long-tailed Duck in the Bolshezemelskaya tundra. Oil-spills during transportation by sea may also be an important factor of decline in the Long-tailed Duck population. Meanwhile, in the Malozemelskaya tundra, which did not experience oil and gas development, the breeding population over the last decades remained stable. Urgent establishment of new protections in key breeding areas in Arctic Russia, sustainable population management, and new research programs are necessary for the conservation and enhancement of this globally threatened species.

Habitat suitability mapping of white stork Ciconia ciconia in one of its key European breeding areas

Due to rapid changes of the agricultural practice, the traditionally managed farmland became currently-one of the most endangered habitats in Europe. Species related to the rural landscape have been facing a great challenge of adaptation to quickly changing conditions. Therefore, recognizing and characterizing highly suitable areas for white storks is very important to plan conservation measures in the era of changes in agriculture and land use. Here, combining nest survey data (811 occupied nest), GIS-data on habitat availability and modelling approach, we characterize the current foraging conditions of the white stork Ciconia ciconia, an indicator of the agricultural habitat biodiversity and an umbrella species for organisms associated with agriculture landscape. The studied population breeds in the Warmińska Refuge Natura 2000 site (N Poland), one of the key breeding areas of this species in Europe. Breeding pair presence was predicted by the area of pasture, meadows, field ponds, and linear water within a 1 km buffer around the nest. The main hotspots of habitat suitability were located in the central and western parts of the study area, characterized by a more traditional model of agriculture. The distance to important foraging habitats does not influence white stork fecundity indicating that landscape composition is important when choosing the breeding site. The pairs with higher number of young were located further from other neighbouring pairs and at the areas with lower density of pairs in general. This is probably linked to the lower competition for food between more distant breeding pairs. Our results show that the traditional agricultural use in mosaics of pastures, meadows and aquatic habitats promotes white storks nesting.

Emergence phenology of the giant salmonfly and responses by birds in Idaho river networks

Emergence of adult aquatic insects from rivers is strongly influenced by water temperature, and emergence timing helps to determine the availability of this ephemeral food resource for birds and other terrestrial insectivores. It is poorly understood how spatial heterogeneity in riverine habitat mediates the timing of emergence. Such spatiotemporal variation may have consequences for terrestrial insectivores that rely on aquatic-derived prey resources. We investigated emergence phenology of the giant salmonfly, Pteronarcys californica, at three spatial scales in two Idaho river networks. We examined the influence of tributary confluences on salmonfly emergence timing and associated insectivorous bird responses. Salmonfly emergence timing was highly variable at the basin-scale during the period we sampled (May–June). Within sub-drainage pathways not punctuated by major tributaries, emergence followed a downstream-to-upstream pattern. At the scale of reaches, abrupt changes in thermal regimes created by 10 major tributary confluences created asynchrony in emergence of 1–6 days among the 20 reaches bracketing the confluences. We observed 10 bird species capturing emerged salmonflies, including 5 species typically associated with upland habitats (e.g., American robin, red-tailed hawk, American kestrel) but that likely aggregated along rivers to take advantage of emerging salmonflies. Some birds (e.g., Lewis’s woodpecker, western tanager, American dipper) captured large numbers of salmonflies, and some of these fed salmonflies to nestlings. Emergence asynchrony created by tributaries was associated with shifts in bird abundance and richness which both nearly doubled, on average, during salmonfly emergence. Thermal heterogeneity in river networks created asynchrony in aquatic insect phenology which prolonged the availability of this pulsed prey resource for insectivorous birds during key breeding times. Such interactions between spatial and temporal heterogeneity and organism phenology may be critical to understanding the consequences of fluxes of resources that link water and land. Shifts in phenology or curtailment of life history diversity in organisms like salmonflies may have implications for these organisms, but could also contribute to mismatches or constrain availability of pulsed resources to dependent consumers. These could be unforeseen consequences, for both aquatic and terrestrial organisms, of human-driven alteration and homogenization of riverscapes.

Community-Managed Fish Sanctuaries for Freshwater Fishery Biodiversity Conservation and Productivity in Malawi

Key fish breeding and other biodiverse areas in Malawian lakes are under threat from illegal fishing, the siltation of key breeding areas (due to deforestation-induced soil erosion), and the clearing of shoreline aquatic vegetation. Freshwater protected areas, also called sanctuaries, have the potential to support the restoration of degraded aquatic environments and protect fisheries’ biodiversity. In Malawi, community-managed fish sanctuaries have been established by beach village committees (BVCs) throughout Lake Malawi, Lake Malombe, Lake Chilwa and Lake Chiuta. The sanctuaries were established to conserve exploited stocks, preserve biodiversity, and enhance fisheries’ yield. The BVCs are aligned with local decentralized village development committees linked to District Councils. Together, they constitute a defragmented decentralized ecosystem-based management of fishery resources. A monitoring study was conducted in sanctuaries in the four lakes during the wet and dry season over three years (2016–2019). The monitoring was carried out to evaluate the sanctuaries’ biological performance. The results showed that community-managed sanctuaries contributed to a 24% increase in the total number of observed species. The Shannon Diversity Index increased from an average 1.21 to 1.52. Small and mid-size (<50 ha) sanctuaries showed a higher performance improvement than large (>50 ha) sanctuaries. This is likely due to multiple factors, including a higher level of fish movement and the greater ability of communities to surveil and enforce smaller sanctuaries. The participation of communities in monitoring enhanced the demonstration effects of sanctuaries. This, in turn, encouraged communities to expand the number and size of the sanctuaries. The biological performance results indicate that community-managed freshwater sanctuaries can be used to protect and restore fish biodiversity in freshwater lakes in Africa. Linking the BVCs to defragmented decentralized structures ensures that the interconnectedness between ecosystem uses, including forestry, agriculture, and tourism, which impinge on fish productivity, are addressed holistically.

Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Cinnamomum camphora (‘Gantong 1’)

Cinnamomum camphora is one of the most commonly used tree species in landscaping. Improving its ornamental traits, particularly bark and leaf colors, is one of the key breeding goals. The basic helix-loop-helix (bHLH) transcription factors (TFs) are crucial in controlling anthocyanin biosynthesis in many plants. However, their role in C. camphora remains largely unknown. In this study, we identified 150 bHLH TFs (CcbHLHs) using natural mutant C. camphora 'Gantong 1', which has unusual bark and leaf colors. Phylogenetic analysis revealed that 150 CcbHLHs were divided into 26 subfamilies which shared similar gene structures and conserved motifs. According to the protein homology analysis, we identified four candidate CcbHLHs that were highly conserved compared to the TT8 protein in A. thaliana. These TFs are potentially involved in anthocyanin biosynthesis in C. camphora. RNA-seq analysis revealed specific expression patterns of CcbHLHs in different tissue types. Furthermore, we verified expression patterns of seven CcbHLHs (CcbHLH001, CcbHLH015, CcbHLH017, CcbHLH022, CcbHLH101, CcbHLH118, and CcbHLH134) in various tissue types at different growth stages using qRT-PCR. This study opens a new avenue for subsequent research on anthocyanin biosynthesis regulated by CcbHLH TFs in C. camphora.

CONTRIBUTION OF LOCAL URBAN PARKS IN PROLIFERATION OF DENGUE VECTORS IN KUALA LUMPUR, MALAYSIA

The importance of urban parks in the transmission of dengue fever should not be underestimated, and such parks should be incorporated into existing vector control initiatives. Our research seeks to identify the features of containers in major public parks in the city of Kuala Lumpur, Malaysia where Aedes sp. mosquitoes breed. Additionally, this study utilized spatial analysis to create a map of the geographical distribution of Aedes sp. breeding sites. Five primary and popular parks in Kuala Lumpur located within a 400-metre radius of dengue outbreak areas in 2018 were chosen based on their high number of visitors. An entomological survey was carried out, and the coordinates and characteristics of water containers were documented. Average Nearest Neighbourhood (ANN) and Kernel Density estimation methods were utilized to assess the spatial distribution of Aedes sp. breeding. The ANN results indicated that the observed mean distance of Aedes sp. breeding was 35.55 metres for BP, 61.19 metres for TM, 67.77 metres for TT, 110.14 metres for KM and 25.43 metres for AD. Based on the z-score calculation, this study discovered a clustered breeding pattern at BP, TM and AD; a dispersed pattern was observed at TT, and a random pattern was detected at KM. Kernel Density estimation was applied to generate hotspot maps for each park. Two factors that were significantly associated with the abundance of Aedes sp. larvae were identified, which include the presence of rainwater (aOR=21.89, 95% CI=6.54-73.20) and the absence of a roof (aOR=4.19, 95% CI=2.38-7.37). By mapping dengue vectors and identifying key breeding containers and their features, this study serves as a valuable resource for public park management to establish focused vector control efforts.

Plastidial Phosphoglucomutase (pPGM) Overexpression Increases the Starch Content of Transgenic Sweet Potato Storage Roots.

Sweet potato (Ipomoea batatas), an important root crop, has storage roots rich in starch that are edible and serve as a raw material in bioenergy production. Increasing the storage-root starch contents is a key sweet potato breeding goal. Phosphoglucomutase (PGM) is the catalytic enzyme for the interconversion of glucose-6-phosphate and glucose-1-phosphate, precursors in the plant starch synthetic pathway. Plant PGMs have plastidial and cytosolic isoforms, based on their subcellular localization. Here, IbpPGM, containing 22 exons and 21 introns, was cloned from the sweet potato line Xu 781. This gene was highly expressed in the storage roots and leaves, and its expression was induced by exogenous sucrose treatments. The mature IbpPGM protein was successfully expressed in Escherichia coli when a 73-aa chloroplastic transit peptide detected in the N-terminus was excised. The subcellular localization confirmed that IbpPGM was localized to the chloroplasts. The low-starch sweet potato cultivar Lizixiang IbpPGM-overexpression lines showed significantly increased starch, glucose, and fructose levels but a decreased sucrose level. Additionally, the expression levels of the starch synthetic pathway genes in the storage roots were up-regulated to different extents. Thus, IbpPGM significantly increased the starch content of the sweet potato storage roots, which makes it a candidate gene for the genetic engineering of the sweet potato.

Mapping and identification of quantitative trait loci controlling test weight and seed yield of pearl millet in multi agro-climatic zones of India

Pearl millet [ Pennisetum glaucum (L.) R. Br.] is a climate-resilient nutri-cereal and is a staple food for the inhabitants of arid and semi-arid regions of the world. Yield stability is a major problem and requires exploiting key breeding strategies for the improvement of yield component traits in pearl millet. The main objective of the present study was the genomic dissection of yield and its component traits by identifying multi-environmental QTL in order to increase the efficiency and accuracy of pearl millet breeding. An experiment was designed for mapping agronomically important traits in 210 Recombinant inbred lines (RIL) derived from the cross PPMI 683 × PPMI 627. These RILs were evaluated in three diverse pearl millet growing regions in India for three consecutive years. Over the consecutive years and locations, thousand seed weight (TSW) showed a significant positive association with other agronomic traits. QTL analysis revealed three significant common QTL for TSW. the flanking markers of common QTL were Xpsmp2273- Xipes0203; Xpsmp2077- Xpsmp2059 and ICMP3058- Xipes0147 . The identified common QTL markers explained the total phenotypic variance of 27.57, 22.61,7.59% for QTL 1 on LG 1; 21.38, 24.13,12.14% for QTL 2 on LG 2, and 7.34, 15.26, 9.6% for QTL 3 on LG 6 across three consecutive years (2014–2016) at Delhi (E1), Dharwad (E2) and Jodhpur (E3), respectively. Two constitutive expressing QTL markers for Seed Yield per Plant (SYPP) were found at a significant threshold LOD value of 3.5 and flanked by the markers: Xpsmp2273- Xipes0203 and Xpsmp2077- Xpsmp2059 with a total phenotypic variance of 28.24 , 19.95%, and 6.31% for QTL 1 on LG 1; 19.78, 21.38, 7.17% for QTL 2 on LG 2 across consecutive years at Delhi, Dharwad and Jodhpur, respectively. In total, 34 and 29 significant digenic interactions were detected for TSW and SYPP, respectively. In the present study, using quantitative genetic variation for TSW and SYPP, major and stable QTLs were found across environments. Some potential genes that may affect the traits were identified in the comparative genomics scan using rice and Arabidopsis. Three significant and stable QTLs for TSW and two for SYPP were detected across all environments. The digenic interactions were detected for TSW (34) and SYPP (29) at Delhi, Dharwad, and Jodhpur. The mapped QTL for TSW and SYPP in the current study could be exploited to develop elite hybrid parental genotypes/cultivars through marker-assisted selection and genomic selection in breeding programs. • In an era of climate change, pearl millet has promising prospects to achieve economic returns. • Major and stable QTLs for TSW (3 QTLs) and SYPP (2 QTLs) were detected across the environments. • Two genomic regions with pleiotropic effects for TSW and SYPP at Delhi, Dharwad, and Jodhpur were detected. • Digenic interactions were detected for TSW (34) and SYPP (29) at Delhi, Dharwad, and Jodhpur. • All favorable QTLs to break down genetic barriers to yield for sustainable food security.

Invertebrate abundance increases with vegetation productivity across natural and agricultural wader breeding habitats in Europe

Grassland breeding waders have been steadily declining across Europe. Recent studies indicating a dramatic decline in grassland invertebrates' abundance and biomass, the key food of most grassland wader chicks, suggest a likely driver of the demise of waders. While agricultural intensification is generally inferred as the main cause for arthropod decline there is surprisingly little information on the relationship between land use intensity and total arthropod abundance in grasslands. Here, we explored those relationships across several key wader breeding habitats by surveying ground-active, aerial and soil-dwelling invertebrate communities in five European countries that range from natural undisturbed bogs to intensively managed grasslands. Using maximum vegetation growth and soil moisture content we investigated how they shape the size of the invertebrate community within and across different countries. We found predominantly positive relationships between grassland invertebrate abundance, biomass and body weight with increasing vegetation growth and soil moisture. Maximum vegetation growth was strongly positively related to ground-active invertebrate abundance and biomass and abundance of soil dwelling invertebrates (mainly earthworms). Body weight of aerial invertebrates furthermore increased with increasing maximum vegetation growth. Our results provide little support for the hypothesis that agricultural practices associated with intensification of grassland management result in an abundance decline of invertebrate prey for wader chicks. Conservation practices aiming to enhance wader chick survival require a careful balancing act between maintaining habitat productivity to secure high prey abundance, and keeping productivity low enough to maintain open swards that do not need to be cut before chicks have fledged.

The Past, Present, and Future of Host Plant Resistance in Cotton: An Australian Perspective.

Cotton is a key global fiber crop. However, yield potential is limited by the presence of endemic and introduced pests and diseases. The introduction of host plant resistance (HPR), defined as the purposeful use of resistant crop cultivars to reduce the impact of pests and diseases, has been a key breeding target for the Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program. The program has seen success in releasing cultivars resistant to Bacterial blight, Verticillium wilt, Fusarium wilt, and Cotton bunchy top. However, emerging biotic threats such as Black root rot and secondary pests, are becoming more frequent in Australian cotton production systems. The uptake of tools and breeding methods, such as genomic selection, high throughput phenomics, gene editing, and landscape genomics, paired with the continued utilization of sources of resistance from Gossypium germplasm, will be critical for the future of cotton breeding. This review celebrates the success of HPR breeding activities in the CSIRO cotton breeding program and maps a pathway for the future in developing resistant cultivars.

The bHLH transcription factor AcB2 regulates anthocyanin biosynthesis in onion (Allium cepa L.).

Onion bulb color is a key breeding trait. The red bulb color is caused by the presence of anthocyanins, which are products of the flavonoid synthesis pathway. Research on flavonoid regulation in onion is lagging compared with that in other crops. AcB2 encodes a basic helix–loop–helix (bHLH) transcription factor, and its transcription is positively associated with anthocyanin accumulation and correlated with the expression of AcMYB1, which is an activator in the flavonoid biosynthetic pathway in onion. Phylogenetic analysis showed that AcB2 was grouped into the TRANSPARENT TESTA 8 (TT8) clade of the bHLH IIIf subgroup. The AcB2 protein contained an MYB-interacting region and physically interacted with AcMYB1 in yeast and tobacco leaves. AcMYB1 directly bound to the promoters of anthocyanidin synthase (AcANS) and flavonoid 3-hydroxylase 1 (AcF3H1) and activated their expression. The coexpression of AcB2 with AcMYB1 in Arabidopsis thaliana protoplasts dramatically increased the expression of AcANS and AcF3H1 compared with that under the expression of AcMYB1 alone. Transient co-overexpression of AcB2 with AcMYB1 induced anthocyanin accumulation in the epithelial cells of onion bulbs. Complementation of the Arabidopsis tt8-1 mutant with AcB2 restored pigmentation defects in tt8-1. In addition, AcB2 physically interacted with AtTT2 in yeast cells and tobacco leaves, indicating that the functions of AcB2 were similar to those of AtTT8. Together, these results demonstrated that AcB2 enhanced the function of AcMYB1 in upregulating anthocyanin biosynthesis in onion, which provides a theoretical basis for breeding onions with higher anthocyanin contents.

Influence of genotype and environment on grain yield among cowpea (Vigna unguiculata (L.) Walp) genotypes under dry land farming system

ABSTRACT The identification of high-yielding and stable genotypes for cultivation across differential production regions is among the key breeding objectives in cowpea improvement programs. This study was aimed to determine genotype-by-environment interaction (GEI) for grain yield to select high-yielding and stable cowpea genotypes for production in South Africa and identical agro-ecologies, and for cultivar development. Fifty cowpea genotypes were tested for grain yield across seven environments of South Africa using a 10 × 5 alpha lattice design replicated three times, during the 2019/2020 and 2020/2021 planting seasons. Grain yield data were subjected to analysis of variance (ANOVA), additive main effects and multiplicative interaction (AMMI) and the genotype-by-environment interaction (GGE) biplot analyses. ANOVA and AMMI showed significant genotype, environment and GEI effects. High grain yield was recorded for genotypes G35 (0.47 t ha−1), G1 (0.45 t ha−1) and G47 (0.43 t ha−1) across test environments. AMMI stability values (ASV); identified Acc-Cowp44 as the most stable genotype across all sites, recording the lowest ASV of 0.03. The comparison view of GGE biplot revealed Acc-Cowp29, Acc-Cowp38 and Acc-Cowp5 as ideal genotypes, possessing high grain yield of 0.19, 0.47 and 0.36 t ha−1, respectively. The identified genotypes are recommended for production and inclusion in subsequent breeding activities.

Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits.

Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen’s safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1–6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal–human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.

Insights into the fish biodiversity and fishing practices in Shanir Haor of Bangladesh

Despite Bangladesh's attempt to safeguard natural water bodies and wetlands, the loss of aquatic biodiversity is becoming an alarming issue. As a key habitat and breeding ground for inland freshwater fish, Shanir Haor in Bangladesh's north-eastern zone harbors a wide variety of fish species. Recent trends in biodiversity loss have emphasized the indispensable need for comprehensive biodiversity research, which is necessary for evaluating the haor ecosystem's present status and assuring its long-term management. The study intends to portray the present scenario of fish biodiversity and fishing practices in the Shanir Haor ecosystem. A total of 78 fish species were found in the study area, with 26 species commonly available, 22 species moderately available, 22 species rarely available, and 8 species very rarely available. The study identified a variety of natural and anthropogenic factors responsible for decline of fish biodiversity. The research will serve as a baseline for future biodiversity conservation and management in Shanir Haor.

Favorable spring conditions can buffer the impact of winter carryover effects on a key breeding decision in an Arctic-breeding seabird.

The availability and investment of energy among successive life‐history stages is a key feature of carryover effects. In migratory organisms, examining how both winter and spring experiences carryover to affect breeding activity is difficult due to the challenges in tracking individuals through these periods without impacting their behavior, thereby biasing results.Using common eiders Somateria mollissima, we examined whether spring conditions at an Arctic breeding colony (East Bay Island, Nunavut, Canada) can buffer the impacts of winter temperatures on body mass and breeding decisions in birds that winter at different locations (Nuuk and Disko Bay, Greenland, and Newfoundland, Canada; assessed by analyzing stable isotopes of 13‐carbon in winter‐grown claw samples). Specifically, we used path analysis to examine how wintering and spring environmental conditions interact to affect breeding propensity (a key reproductive decision influencing lifetime fitness in female eiders) within the contexts of the timing of colony arrival, pre‐breeding body mass (body condition), and a physiological proxy for foraging effort (baseline corticosterone).We demonstrate that warmer winter temperatures predicted lower body mass at arrival to the nesting colony, whereas warmer spring temperatures predicted earlier arrival dates and higher arrival body mass. Both higher body mass and earlier arrival dates of eider hens increased the probability that birds would initiate laying (i.e., higher breeding propensity). However, variation in baseline corticosterone was not linked to either winter or spring temperatures, and it had no additional downstream effects on breeding propensity.Overall, we demonstrate that favorable pre‐breeding conditions in Arctic‐breeding common eiders can compensate for the impact that unfavorable wintering conditions can have on breeding investment, perhaps due to greater access to foraging areas prior to laying.