Morphometric Traits Research Articles

The Tunisian Barbary Sheep: Correlations among Morphometric Traits in Purebred Ewes Maintained under Arid Conditions

Background: The fat-tailed Barbary sheep are the main breed of Tunisia and their morphometry has not been deeply investigated. This study aims to estimate the degree of relationship between eight quantitative measures across eight age classes, from one to eight years. Methods: Pearson’s product-moment was calculated to evaluate the correlation among eight morphological measures, collected from 249 purebred Tunisian Barbary ewes reared under arid climate. Result: The magnitude of pairwise phenotypic correlation among morphological traits showed a strong positive correlation (r = 0.84, P less than 0.001) between the shoulder and rump height at 6-7 years. The body weight was highly correlated to the height at rump during the first five years of age, whereas, it becomes more correlated to the heart girth when the ewe reaches its heavyweight at 5-6 years and older. The results of this study indicated that the rump height is the most correlated parameter to BW during the early life of this fat-tailed breed and are encouraging to fit live body weight from morphometric traits with accuracy.

Bi-Pinnate Compound Serianthes nelsonii Leaf-Level Plasticity Magnifies Leaflet-Level Plasticity.

Simple SummaryTrees are not able to move in order to avoid stressful conditions. Therefore, trees have developed elaborate methods for modifying their organs to benefit the tree under prevailing conditions. For low light and high light conditions, most studies have looked at how the leaf blade is modified. We have shown that the entire leaf should be observed for modifications rather than just the leaf blade.Numerous leaf traits exhibit developmental plasticity in response to irradiance, an attribute that maximizes performance in the prevailing light. The use of leaflets to represent whole leaf traits of tree species with compound leaves is common in the acclimation literature. These methods ignore the potential for whole leaf plasticity to augment leaflet plasticity. We grew Serianthes nelsonii plants in incident light ranging from 6% to 100% of sunlight and quantified numerous leaflet and leaf traits to determine plasticity index (PI: (maximum-minimum)/maximum)) of each. Leaflet acclimation such as changes in length of palisade mesophyll occurred as expected. However, leaf-level morphometric traits such as rachillae insertion angle also exhibited acclimation potential. The leaf-level plastic behavior enabled acclimation approaches that simple-leaved species do not possess. We illuminate the need to look at the entire leaf when quantifying acclimation potential of tree leaves, and indicate that the historical use of leaflets to represent species with compound leaves under-estimated the acclimation potential when compared to species with simple leaves.

Effects of geoclimatic factors on the variability in Pinus pinea cone, seed, and seedling traits in Turkey native habitats

BackgroundStone pine (Pinus pinea L.) is harvested for its edible kernels. It is an important forest tree species, and also plays an important role in afforestation. Successful afforestation activities strongly depend on the quality of seeds and seedlings. Five eastern native populations of stone pine were analyzed, in terms of their geographical and climatic parameters, in order to identify their cone, seed, pine nut, and seedling traits. With this regard, we aimed to contribute to the reforestation, yield, and breeding of this species.ResultsAll native populations occur in the sub-humid bioclimatic zone, according to Emberger’s bioclimatic classification, ranging 74.7–63.2 of Emberger’s Q Index value (Q), which synthesizes humidity and temperature, with lower values indicating more arid conditions. With regard to geographical factors, altitude was found to have the greatest effect on cone diameter and seed weight, while there was a weak correlation of cone, seed, and pine nut dimension with longitude and latitude. In terms of climatic factors, Q and mean of the maximum temperature of June, July, and August (ME) were found to be the main drivers behind significant effects in cone, seed, and pine nut morphometric traits. The most negative effect on seed number cone−1 (r: − 0.897), pine nut number cone−1 (r: − 0.923), pine nut yield (r: − 0.903), and pine nut weight (r: − 0.878) was Q, whereas cone diameter, seed length, and seed weight were positively correlated with the ME (r: 0.939, r: 0.889, and r: 0.866, respectively). Cone and seed diameter and seed weight increased with decreasing summer drought index (r: − 0.806, r: − 0.846, and r: − 0.866, respectively). Rainfall in the June of the third year prior to harvest time (RJ) had a negative effect on the percentage of sound seeds per cone. Annual rainfall in the third year prior to harvest time (AR) significantly affected pine nut weight (r: 0.889), although rainfall during summer had a negative effect. The empty seed ratio of the different populations ranged from 20 to 68%, while considering all populations, the empty seed ratio was 46%.ConclusionsThe study suggests that the Q Index and ME should be taken into account to determine cone to pine nut yield. With this regard, plantations of stone pine should be established on sub-humid areas and Q values should not exceed 75.

Functional traits of leaves and photosynthetic stems of species from a sarcocaulescent scrub in the southern Baja California Peninsula.

Photosynthetic stems represent a source of extra carbon in plants from hot and dry environments, but little is known about how leaves and photosynthetic stems differ in terms of photosynthetic capacity, trait coordination, and responses to seasonal drought in subtropical systems. We studied photosynthetic, hydraulic, morphometric (specific leaf area [SLA], wood density [WD]), and biochemical (C and N isotopes) traits in leaves and photosynthetic stems of 12 plant species from a sarcocaulescent scrub in the southern Baja California Peninsula, Mexico, in wet and dry seasons. Leaves and stems had similar mean photosynthetic capacity, as evaluated by chlorophyll fluorescence traits, indicating similar investment in leaf and stem photosynthesis. We did not find a relationship between stem hydraulic conductivity and leaf or stem photosynthetic traits. However, we found resource allocation trade-offs, between WD and both stem hydraulic conductivity and SLA. Leaf and stem photosynthetic traits did not change with season, but specific stem area was one of the few traits that changed the most between seasons-it increased during the dry season by as much as 154% indicating substantial water storage. Our results indicate the same proportional investment in photosynthetic capacity and dry matter in both leaves and photosynthetic stems across all 12 species. We identified multiple strategies at this seasonal site, with species ranging from high WD, low SLA, low hydraulic conductivity, and high specific bark area on one end of the spectrum and opposite traits on the other end.

How does the stand structure of treeline-forming species shape the treeline ecotone in different regions of the Nepal Himalayas?

Stand structure dynamics are considered as major happenings in any forest as a response to environmental changes. However, this important topic is underrepresented in the treeline studies in the Nepal Himalayas. We aimed to investigate site- as well as species-specific changes in morphometric features (basal diameter, crown cover, density, and height) along the elevational gradient across treeline ecotones in response to recent environmental changes. The stand structure characteristics of Abies spectabilis, Pinus wallichiana, and Betula utilis across the treeline ecotone of three study sites in Eastern (Barun), Central (Manang), and Western (Dhorpatan) Nepal were analyzed to elucidate structural heterogeneities. Altogether, eight transects (20 m × (60–250 m)) across the treeline ecotone were established. Trees of all life forms, trees (> 2 m), saplings (0.5–2 m), and seedlings (< 0.5 m), within each transect were enumerated and sampled for the morphometric features and age. Site-specific and species-specific stand structure dynamics were found. The rate of basal area increment was higher in Barun, but the Manang treeline, despite profound regeneration in recent years, had a low annual basal area increment. Moreover, the altitudinal distribution of age and morphometry were not consistent among those ecotones. Furthermore, intra-specific competition was not significant. The site-specific stand structure dynamics explain why treelines do not respond uniformly to increasing temperature. It invokes, in further studies, the incorporation of the tree’s morphometric adaptation traits, phenotypic plasticity, and interactions between species genotype and the environment.

First Report of Pratylenchus penetrans (Nematoda: Pratylenchidae) Associated with Amaryllis (Hippeastrum × hybridum), in Portugal

The world flower business is a highly dynamic industry and in Portugal yields around EUR 500 million a year (INE 2013). Root lesion nematodes (RLNs), Pratylenchus spp., are considered the third most important group of plant parasitic nematodes (PPNs) worldwide due to their large distribution, wide host range, and impact on economically important crops (Castillo and Vovlas 2007). The most recent report of RLNs parasitizing amaryllis (Hippeastrum spp.) was the amaryllis lesion nematode, Pratylenchus hippeastri, in Florida (U.S.A.) (Gozel et al. 2007). In 2016, soil and root samples of amaryllis hybrid Hippeastrum × hybridum cv. Benfica were collected from potted plants produced in greenhouses in Montijo (Setubal Peninsula, Central Portugal), 50 km from Lisbon. Nematodes were extracted from soil samples according to the protocol PM 7/119 (1) (EPPO 2013) and identified to genus level based on morphometrical traits of 10 females and 11 males. DNA extraction was conducted from 10 nematodes separately, followed by PCR amplification and sequencing of the D2/D3 expansion segment of the 28S rRNA and 18S rRNA genes using the primers D2A and D3B (Nadler et al. 1999) and 1813F and 2646R (Holterman et al. 2006). The nucleotide sequences were deposited as MN756841 and MN756509 at the NCBI. RLNs were detected in all five samples in a concentration of around 100 nematodes/100 cm³ of soil. Some primary roots of affected plants showed small, elliptical, reddish-brown lesions and poor growth. More severely affected plants presented stunted, chlorotic foliage and had the cortical lesions enlarged to the point that rotting was severe and many roots were easily detached from the bulb; in some cases, there was not emergence from bulbs. The female body was moderately slender, almost straight when killed by gentle heat, lateral field with four straight lines, body annules distinct, lip with three annules, stylet knobs round, median bulb round, spermatheca round and filled with sperm, tail tapering to rounded terminus, sometimes with two striae. Body length was 558.99 ± 48.50 μm, body width 22.45 ± 2.02 μm, stylet length 18.52 ± 1.02 μm, and tail length 32.91 ± 7.50 μm. Values of a, c, and c′ ratios were 25.95 ± 2.53, 17.62 ± 3.45, and 38.49 ± 4.42; V (%) value was 80.92 ± 1.69. Males were smaller than females with body length 511.37 ± 29.90 μm, stylet length 17.55 ± 1.04 μm, and spicule length 18.53 ± 1.17 μm. No other PPN was found in the suspensions extracted from the soil samples. BLAST hits showed that partial sequence of D2/D3 rRNA loci (540 bp) was 96.2% identical (e-value 0.0) to Pratylenchus penetrans isolate MU2 (KP161612) and voucher T143 (KY828357). The partial sequence of 18S rRNA (650 bp) was 100% identical to P. penetrans isolate ILVO-Pp (MH983023) and 99.81% to P. penetrans Praty-A (AB661627). In the corresponding phylogenetic trees, both P. penetrans sequences clustered together with other species from the penetrans group (P. fallax, P. convallariae, and P. oleae) with good support (Janssen et al. 2017). Nevertheless, although all species within this group share many morphological characteristics (Subbotin et al. 2008), our specimens presented higher similarity, both morphological and molecular, with P. penetrans. So far, this RLN has been found associated mainly with potato fields in Portugal (Abrantes et al. 1987; Esteves et al. 2015); thus, to our knowledge, this is the first report of P. penetrans parasitizing amaryllis, in Portugal.

Gamma radiosensitivity study on wheat (Triticum turgidum ssp. durum)

Abstract Fifty wheat seed variety (var.) CIRNO C2008 were gamma irradiated with 100, 200, 300, 400, 500, or 600 Gy by using a Cobalt-60 source at 907.39 Gy/h, and the nonirradiated seeds were considered the control (M 0). A photoperiod of 13 h of darkness (14°C) and 11 h of light (2 h at 18°C, 7 h at 25°C, and 2 h at 18°C) was used for 30 days, in a growth chamber (BJPX-A450; BIOBASE) for quantifying the morphometric traits of the irradiated vs nonirradiated seeds. The germination percentage (from 88.89% in M 0 to 77.78% in 600 Gy) did not show significant differences among treatments; while the survival percentage (from 100% in M 0 to 6.66% in 600 Gy) and plant height (from 19.21 cm in M 0 to 1.16 cm in 600 Gy) showed negative significant (p &lt; 0.05) difference among nonirradiated seeds (M 0) and the rest of the treatments. Finally, based on the survival percentage, the calculated lethal dose was 290.6 Gy, which will allow obtaining promising wheat mutants. Gamma irradiation is a promising alternative to obtain a greater wheat variability for advanced mutant lines.

Population connectivity of the hydrothermal-vent limpet Shinkailepas tollmanni in the Southwest Pacific (Gastropoda: Neritimorpha: Phenacolepadidae).

The Southwest Pacific represents an independent biogeographic province for deep-sea hydrothermal vent fauna. Different degrees of genetic connectivity among vent fields in Manus, North Fiji and Lau Basins have been reported for various molluscan and crustacean species, presumably reflecting their different levels of dispersal ability as swimming larvae. The present study investigates the population connectivity of the hydrothermal vent limpet Shinkailepas tollmanni (family Phenacolepadidae) in the Southwest Pacific. Our analyses using mitochondrial COI-gene sequences and shell morphometric traits suggest a panmictic population structure throughout its geographic and bathymetric ranges, spanning 4,000 km from the westernmost Manus Basin (151ºE; 1,300 m deep) to the easternmost Lau Basin (176ºE; 2,720 m). The measurements of its embryonic and larval shells demonstrate that the species hatches as a planktotrophic veliger larva with an embryonic shell diameter of 170–180 μm and settles at the vent environment with the larval shell diameter of 750–770 μm. This substantial growth as a feeding larva, ca. 80 times in volume, is comparable or even greater than those of confamilial species in the hydrothermal-vent and methane-seep environments in the Northwest Pacific and Atlantic Oceans. Large pigmented eyes in newly settled juveniles are another common feature in this and other phenacolepadids inhabiting the chemosynthetic environments. These results put together suggest that the larvae of S. tollmanni migrate vertically from deep-sea vents to surface waters to take advantages of richer food supplies and faster currents and stay pelagic for an extended period of time (> 1 year), as previously indicated for the confamilial species.

Resistance of genetically modified wheat plants, containing a double-stranded RNA suppressor of the

Aim. Analysis of physiological and biochemical characteristics and grain productivity traits of transgenic common wheat plants (Triticum aestivum L.) with a double-stranded RNA suppressor of the proline dehydrogenase gene (pdh) compared to non-transgenic genotypes under conditions of soil drought. Methods. Biochemical assays: spectrophotometric measurements of antioxidant enzymes (SOD, APX) activity, proline dehydrogenase activity and free L-proline content; biotechnological assays: Agrobacterium-mediated transformation in planta; physiological: morphometric traits and elements of grain productivity; mathematical statistics. Results. The presence of a double-stranded RNA suppressor of the gene pdh in transgenic plants leads not only to a decrease in enzyme activity (on average 2 times compared to the nontransgenic plants), but also to an increase in the content of free L-proline both under optimal conditions and under soil drought (2.6–4.1 times). Under soil moisture defi ciency, transgenic plants with reduced pdh gene activity in terms of yield structure signifi cantly exceeded the corresponding values of grain productivity elements for the non-transformed ones. In terms of the grain weight from the main stem, the biotechnological plants under soil moisture defi ciency exceeded the control plants 1.5–1.6 times, while the number of grains did not differ signifi cantly. The grain productivity of the whole plant in the transformed lines under conditions of soil moisture defi ciency was somewhat inferior to those in the nontransformed plants grown under optimal conditions. Soil drought caused a signifi cant increase in SOD and APX activity (by 40 and 11 %, respectively) in plants of the original variety. On the contrary, the activity of both antioxidant enzymes under drought conditions in transgenic plants decreased: SOD – down to 73–76 %, APX – down to 82–86 %, compared with the variant of 70 % of fi eld capacity. Conclusions. The analysis of physiological and biochemical characteristics, as well as economic and grain productivity elements of transgenic common wheat plants with a double-stranded RNA suppressor of the proline dehydrogenase gene showed their increased tolerance to soil drought, compared with non-transgenic genotypes, which may be associated with higher proline accumulation and an increase in the antioxidant enzymes activity. Under soil moisture defi ciency, transgenic wheat plants with reduced pdh gene activity signifi cantly exceeded the corresponding values of grain productivity elements for non-transformed plants. The analysis of the antioxidant enzymes activity in the chloroplasts of transgenic plants showed that under physiological conditions, the antioxidant system works more actively in comparison with non-transgenic genotypes, which may be a prerequisite for increasing the tolerance of these plants to the infl uence of stressors of various origin. It is likely that the positive relationship between the level of free L-proline and the resistance of transgenic wheat plants to osmotic stress is associated either with the effect of L-proline on the expression of other genes of the stress-strain response of plants, or with the positive effect of the increased content of this amino acid on resistance at the early stages of stress development. It has been suggested that an increase in the antioxidant enzymes activity in biotechnological plants can be caused by the expression of heterologous genes.

Transcriptome-wide genotype-phenotype associations in Daphnia in a predation risk environment.

Phenotypic variation plays an important role in how species cope with environmental challenges. Pinpointing which genes and genomic regions are underlying phenotypic variability thus helps to understand the processes of acclimation and adaptation. We used Daphnia as a system to identify candidates playing a role in phenotypic variation related to a predation risk environment with a genome-wide association approach. Furthermore, a gene co-expression network analysis allowed identifying clusters of co-expressed genes which correlated to life history traits. To enhance the understanding of the functional roles of the transcripts, we identified orthologs and paralogs from related species and used ontologies to annotate the candidates of interest. Our study revealed that only one life history trait and two morphometric traits have a genetic association in the presence of predation risk (fish kairomones), whereas most genotype-phenotype associations were detected in a genotype-environment interaction analysis for reproduction-related phenotypic traits. The gene co-expression network analysis identified a total of 44 modules, of which one module correlated to another life history trait namely the 'total number of broods'. The combined use of gene co-expression network and transcriptome-wide association analysis allowed the identification of 131 candidate transcripts associated with life history traits in Daphnia galeata. These results lay the ground for targeted studies to further understand phenotypic variability in this species.

Sperm Parameters in Pristidactylus achalensis (Squamata: Leiosauridae), a Lizard Endemic to the Highest Mountain Areas in Central Argentina

Reproductive physiology is influenced by environmental pressures, particularly in ectothermic species living in harsh climatic conditions. Studying the period of time in which males exhibit semen availability and their sperm traits constitutes a powerful tool to evaluate the fertility potential of males because sperm size and sperm velocity have been proposed as determinants in fertilization success. Pristidactylus achalensis is a lizard endemic to the highest mountain areas in Central Argentina and shows a pattern of seasonal activity. Here, we study the period of time when males possess sperm during the active season and characterize the spermatozoa based on sperm morphometric and dynamic traits among males and within ejaculate. Males possess sperm in their ejaculates only during the spring months of the active season, suggesting that reproductive activity is restricted to this time. Spermatozoa of Pristidactylus achalensis show intra-specific variation in sperm traits among males and within ejaculate, suggesting different reproductive potential among males. Since this species only occupies the highest areas of the mountains and is categorized as vulnerable, basic information about reproduction and sperm physiology could be useful for potential population conservation strategies.

A 17-bp InDel (rs668420586) within goat CHCHD7 gene located in growth-related QTL affecting body measurement traits.

The Coiled-Coil-Helix-Coiled-Coil-Helix Domain Containing 7 (CHCHD7) gene was located in a growth-related major QTL that participated in the process of bone cells metabolism in animals by regulating mitochondrial copper homeostasis and cytochrome C oxidase assembly. Therefore, we speculated that CHCHD7 gene might be involved in animal growth and body size. Herein, we discovered a 17-bp insertion/deletion (indel) within the goat CHCHD7 gene. Then, we detected this variation in Shaanbei White Cashmere (SBWC, n = 1055) goats and Inner Mongolia White Cashmere (IMWC, n = 743) goats (Alathai type) using the mathematical expectation (ME) method. We then analyzed the correlation between these genotypes and goat body measurement traits. The results showed that the minor allelic frequency (MAF) was 0.011 in SBWC, and 0.048 in IMWC. In SBWC and IMWC, the reaction time by ME method was reduced by 36.78% and 27.59%, respectively, compared to the traditional method of screening samples one by one. Moreover, in SBWC goats, the 17-bp indel was significantly associated with body measurement traits (e.g. body height, and body length) in adults. In IMWC goats, the 17-bp indel was correlated with body measurement traits (e.g. body height) in weaners. In SBWC and IMWC goat populations, the body measurement traits of the individuals homozygous for 17-bp indel were higher than those in heterozygous individuals, except for the case of cannon circumference in IMWC weaners. These findings showed that the 17-bp insertion mutation within the goat CHCHD7 gene significantly affected body morphometric traits, and could provide a basis for marker-assisted selection (MAS) breeding of cashmere goats.

Genotype by environment interaction and genetic parameters for growth traits in the Neotropical fish pacu (Piaractus mesopotamicus)

Pacu (Piaractus mesopotamicus) belongs to the main native fish group of the continental aquaculture in South America. However, breeding programs are not available for this species. The estimation of parameters for different traits and in different environments are needed to set up optimized breeding programs Therefore, the objectives of this study were to estimate genetic parameters, to evaluate genotype by environment (GxE) interaction, and to identify morphotypes for growth traits in pacu, using an experimental data of a pedigreed population in Brazil. Data from 1380 individuals corresponding to 48 full-sib families for ten growth traits (initial weight, final weight, average daily gain, total length, standard length, head length, pelvis length, total height, head height, height at the posterior region) were evaluated in two distinct environments (breeding nucleus: env1; commercial fish farm: env2) at 15 months old. The average of final weight was 591.90 ± 274.60 g in env1 and 1035.80 ± 270.00 g in env2. The heritability estimates were registered as moderate/high, which ranged from h2 = 0.27 ± 0.12 to 0.74 ± 0.19. Correlation values between the growth traits were positive and low-high, ranging between 0.32 ± 0.04 to 0.96 ± 0.10 (phenotypic) and 0.33 ± 0.10 to 0.98 ± 0.01 (genetic). The genetic correlations between final weight and morphometric traits were significant and high (ranging from 0.70 ± 0.10 to 0.88 ± 0.05). Our results also revealed different morphotypes patterns for pacu (elliptical and rounded). GxE interaction was considered low for all traits between the two environments (correlation values of 0.80 ± 0.34 to 0.98 ± 0.23). In conclusion, our results suggest that growth traits can be incorporated into the breeding objective in pacu and superior animals evaluated at the breeding nucleus are predicted to be superior at the commercial environment. Moreover, selection can be driven according to the desired morphotype in pacu.

Sexual dimorphism in Scutiger boulengeri, an endemic toad from the Tibetan Plateau

Abstract The evolution of sexual dimorphism has long fascinated evolutionary biologists and theory suggests that variation in sexual dimorphism is a consequence of selective forces acting differently on morphological traits in males versus females. Here, we analyzed sexual differences in size and shape of the Boulenger’s lazy toad, Scutiger boulengeri, based on the intersex variation pattern of sixteen morphometric traits including body size. The results suggested that sexual dimorphism was apparent in body size and some body shapes (e.g., head length and width, internasal space, interorbital space, diameter of lower arm and tibia width) of this toad. The bigger body size in females may be relevant to fecundity selection, a larger head in males as well as a broader internasal and interorbital space may be subject to male-male competition in combination with ecological selection, and both robust forelimbs and hindlimbs in males may be related to mating and competitive behaviors. These results are discussed with respect to the above selection procedures and possible sex differences in life history traits.

PCR-RFLP Polymorphism of Growth Hormone Gene and Its Association with Growth and Morphometric Traits in Ganjam and Baigani Goats of Odisha

Background: Growth Hormone (GH) gene codes for the growth hormone, an anabolic hormone synthesized and secreted by the somatotroph cells of pituitary. Growth hormone influences many processes such as growth, lactation, reproduction and metabolism. Genetic variation in the gene are utilized as markers for selecting animals that are superior in terms growth, production and reproduction traits. Information available on the polymorphism of growth hormone gene of Ganjam and Baigani goats of Odisha is scanty. The current investigation was done to explore the genetic variation of this gene and its association with morphometric traits. Methods: Genetic polymorphism in exon 2 and 3 of Growth hormone gene in Ganjam goat and Baigani goat was explored with sample size of 100 goats for each. The goats belonged to three locations: Khallikote, Rambha, Chattrapur of Ganjam district. The goats were recorded for their body weights, morphometric traits and morphological traits. Genomic DNA was isolated, the target segment comprising exons 2 and 3 was amplified and PCR-RFLP was carried out using Hae III restriction enzyme. Genotypes were scored. Result: PCR of the locus resulted in 422 bp PCR product. PCR-RFLP using Hae III restriction enzyme yielded only two variants in both the populations. The variant A had only one restriction recognition site on the target gene segment yielding two bands with size of 366bp and 56bp whereas the variant B did not have any restriction site with single band of 422bp. Three genotypes AA, AB and BB were found in both the population. In both the population, the gene and genotype frequency were significantly deviated from the Hardy Weinberg Equilibrium frequency. There was a significant difference in the genotype frequencies of growth hormone gene between Ganjam and Baigani goats. The AB genotype had higher mean value for all morphometric traits than AA and BB genotype though the differences were not found to be significant.

Construction of a high-density genetic linkage map and fine mapping of QTLs for growth and sex-related traits in red-tail catfish (Hemibagrus wyckioides)

High-density genetic linkage map based on single nucleotide polymorphisms (SNPs) are essential for fine mapping of QTLs and identification of trait-related genes in aquaculture fish species. In this study, the first high-density genetic linkage map of red-tail catfish (Hemibagrus wyckioides) based on 2b-RAD sequencing technology was constructed using one F1 family composed of 165 offspring and their parents. A total of 2369 SNP markers were assigned to 29 linkage groups (LGs) and the map spanned 2067.35 cM with an average SNP marker interval of 0.87 cM and genome coverage of 98.16%. QTL mapping analysis revealed that 2 significant and 15 suggestive QTLs for all four morphometric traits were identified on 10 LGs, explaining 7.4–13.3% of phenotypic variations. Some candidate growth-related genes such as ttc39b, lrp1, gng3, aspp2, mgp and rusc2 were identified within QTL intervals, and a SNP in ttc39b was found to be significantly associated with body weight in different genetically unrelated populations of red-tail catfish. In addition, one genome-wide significance sex-related QTL was detected on the LG20 with a contribution to phenotypic variation of 44.2–85.7%. A total of 10 potential sex dimorphic genes, such as vps54, tsg10, pld6, psmd8 and gpa33, were also identified within or near the sex QTL markers in LG20. It suggests that the LG20 may be a sex-related LG in red-tail catfish. This high-density genetic map not only enables us to fine-map these genes related with the economic traits, but also provides effective information for future marker-assisted selection and sex-control breeding in this species.

Determination of body shape and meristic characters variations in wild and cultured populations of cichlid fish, Oreochromis niloticus, from the Republic of Benin, West of Africa

Abstract This study was designed to assess morphological changes between cultured and wild tilapia, Oreochromis niloticus (L.). Wild fish samples were obtained from fishermen operating in the waters of the vicinity of the province Parakou, Benin in November 2014, while the cultured samples were obtained from a fish farm in the municipality of Sô-Ava in the Atlantic region of the southern part of the Republic of Benin. Significant differences were observed in all nine morphometric traits measured. Discriminant analysis of morphometric parameters showed high divergence between the populations. The meristic count, however, overlapped broadly showing no divergence between the populations. The morphometric differences between the cultured and wild tilapia, O. niloticus, could have been linked to genetic differences or environmental factors or a combination of these.

3D characterization of walnut morphological traits using X-ray computed tomography

BackgroundWalnuts are grown worldwide in temperate areas and producers are facing an increasing demand. In a climate change context, the industry also needs cultivars that provide fruits of quality. This quality includes satisfactory filling ratio, thicker shell, ease of cracking, smooth shell and round-shaped walnut, and larger nut size. These desirable traits have been analysed so far using calipers or micrometers, but it takes a lot of time and requires the destruction of the sample. A challenge to take up is to develop an accurate, fast and non-destructive method for quality-related and morphometric trait measurements of walnuts, that are used to characterize new cultivars or collections in any germplasm management process.ResultsIn this study, we develop a method to measure different morphological traits on several walnuts simultaneously such as morphometric traits (nut length, nut face and profile diameters), traits that previously required opening the nut (shell thickness, kernel volume and filling kernel/nut ratio) and traits that previously were difficult to quantify (shell rugosity, nut sphericity, nut surface area and nut shape). These measurements were obtained from reconstructed 3D images acquired by X-ray computed tomography (CT). A workflow was created including several steps: noise elimination, walnut individualization, properties extraction and quantification of the different parts of the fruit. This method was applied to characterize 50 walnuts of a part of the INRAE walnut germplasm collection made of 161 unique accessions, obtained from the 2018 harvest. Our results indicate that 50 walnuts are sufficient to phenotype the fruit quality of one accession using X-ray CT and to find correlations between the morphometric traits. Our imaging workflow is suitable for any walnut size or shape and provides new and more accurate measurements.ConclusionsThe fast and accurate measurement of quantitative traits is of utmost importance to conduct quantitative genetic analyses or cultivar characterization. Our imaging workflow is well adapted for accurate phenotypic characterization of a various range of traits and could be easily applied to other important nut crops.

Understanding genetic variability in the mungbean (Vigna radiata L.) genepool

AbstractMungbean or green gram (Vigna radiata L. Wilczek) is a major pulse crop of Southeast Asia. This is the most liked pulse in India because of its good palatability, nutritional quality and easy digestibility. It is mainly grown in subsistence farming systems in India. The crop species has evolved in a diverse range of agroclimatic conditions and therefore the local germplasm has rich genetic diversity. However, this diversity has not been explored to identify useful traits and germplasm to utilise in crop improvement programmes. Therefore, a study was performed on 1,232 mungbean accessions using 8 quantitative, 18 qualitative traits and 4 seed morphometric traits to understand genetic diversity of the crop and identify trait‐specific germplasm. Wide range of variation was observed for days to flowering, days to maturity, pod length, number of seeds/pod and 100‐seed weight. Relative high phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) was observed for 100‐seed weight, flowering period, seed length and seed breadth. Broad sense heritability (h2) analysis indicated that days to 50% flowering, flowering period, days to 80% maturity, 100‐seed weight and seed‐dimension‐related traits are highly suitable for mungbean breeding programmes. Agglomerative hierarchical clustering analysis based on morphological quantitative traits indicates that the diversity in the mungbean germplasm has no significant relationship with respect to their geographical origin. Principal component analysis (PCA) revealed that the first five principal components (PCs) explained 91.4% of total variation. The maximum variance was explained by PC1 (44.61%) followed by PC2 (21.15%). Plotting of observations in two‐dimensional space corresponding to PC1 and PC2 revealed wide distribution of accessions, and certain accessions were found associated with variables. The agromorphological variability and its genetic nature revealed from this study may prove very useful in ongoing and future breeding programmes.

Comparative Phylogeography and Integrative Taxonomy of Ochlerotatus caspius (Dipera: Culicidae) and Ochlerotatus dorsalis

Given that accurately identifying pathogen vectors is vital for designing efficient mosquito control programs based on the proper surveillance of the epidemiologically important species, it has been suggested the complementary use of independently evolving genes and morphometric traits as a reliable approach for the characterization and delimitation of related species. Hence, we examined the spatial distribution of COI mtDNA and ITS2 rDNA variation from the historical perspective of Ochlerotatus caspius (Pallas, 1771) and O. dorsalis (Meigen, 1830), while simultaneously testing the utility of the two markers in integrative species delimitation when combined with phenotypic character analyses of larvae and adults. Despite the striking difference in haplotype diversity (high in COI mtDNA, low in ITS2 rDNA), no evident phylogeographic structure was apparent in the Palearctic O. caspius. The Holarctic O. dorsalis species was subdivided into two highly distinctive COI mtDNA phylogroups which corresponded to the Nearctic and Palearctic regions. Strong support for the independence of the two allopatric evolutionary lineages suggested that geographical barrier and climatic changes during Pleistocene caused vicariance of the ancestral range. COI mtDNA reliably distinguished O. caspius and O. dorsalis, while ITS2 rDNA yet again lacked the proper resolution for solving this problem. An integrative approach based on the larval and adult morphological traits have varying taxonomic applications due to their differential diagnostic values. Thus, by the implementation of an integrative taxonomic approach, we successfully detected species borders between the two epidemiologically relevant species and uncovered the presence of cryptic diversity within O. dorsalis.