Estimated genetic parameters for growth‐related traits in large yellow croaker Larimichthys crocea using microsatellites to assign parentage

To estimate the heritabilities of growth‐related traits in large yellow croaker, Larimichthys crocea, three independent full‐factorial crosses were created by crossing four males × four females, seven males × three females and four males × three females (set 1, set 2 and set 3). At 13 months post‐hatch, the juveniles were collected from three cross sets and measured for body mass (M), standard length (L_S) and body height (H_B). In addition, the parentage of the juveniles was assigned by genotyping six or seven polymorphic microsatellite loci. Out of the 959 juveniles, 99·6% could be assigned to a single parental pair. Heritabilities of growth‐related traits were estimated for individual and combined sets with the pedigrees reconstructed by using microsatellite genotypes. The heritability estimates at 13 month‐old were 0·02–0·30 for M, 0·02–0·25 for L_S and 0·03–0·36 for H_B. These results showed that the heritabilities of M, L_S and H_B were different among three sets, which suggested that different breeding strategies should be adopted for different sets.     

Mapping quantitative trait loci (QTL) for body weight, length and condition factor traits in backcross (BC1) family of Common carp (Cyprinus carpio L.)

Body weight and length are economical important traits in aquaculture species influenced by quantitative trait loci (QTL) and environmental factors. In this study, a backcross (BC1) common carp family, with 86 progeny, was utilized to construct genetic map for preliminary QTL mapping. The genetic map was constructed with 366 markers, including 191 SNP from gene, coverage 50 linkage groups with an average marker distance of 18.5 cM. A total of fourteen QTLs associated with body weight (BW), body length (BL) and condition factor (K) were detected on ten linkage groups (LGs). Among these QTLs detected, three (qBW8, qBL8 and qK8) were associated with BW, BL and K respectively, were mapped on LG8. qBW8 and qK8 were identified on similar interval neared locus HLJ2394 explained 14.9 and 20.9 % of the phenotype variance, while qBL8 was identified on separate nearby locus HLJ571 with 30.8 % of phenotype variance. Two QTLs, qBW13 and qK13, related with BW and K separately, were found on LG13 at different locus with phenotype variance of 25.3 and 20.9 %. Other two QTLs, qBW19 and qBL19, associated to BW and BL were mapped on same region near SNP0626 on LG19, and explained 10.3 and 15.6 % of phenotype variance. While other seven QTLs related with BW and BL were located on different LGs. Confidential interval was ranged from 1.1 to 10 cM in the present study. These markers, with lower QTL interval, have great influence on the body weight and length. Therefore, these QTLs will be helpful to find out the genes related with specific trait.     

Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea).

RAPD markers were employed for construction of a linkage map and localization of QTLs for oleic acid level using a set of 94 recombinant inbred lines (RILs) of mustard (Brassica juncea L.) as a mapping population. Only 30% of the 235 random primers used were useful in terms of polymorphism detected and the reproducibility of those patterns. Normal Mendelian segregation was observed for the majority of the 130 markers obtained with 71 informative primers; only 13.1% deviated (P < 0.01) from the expected 1:1 ratio. One-hundred and fourteen markers were assigned to 21 linkage groups (LGs) covering a total length of 790.4 cM with an average distance of 6.93 cM between markers. Two quantitative trait loci (QTL) for oleic acid level were mapped to 14- and 10.6-cM marker intervals on two different LGs. Both loci together explained 32.2% of phenotypic variance. One major QTL explained 28.5% of the trait variance observed in this species.     

Gender distribution,sexual size dimorphism and morphometric sexing in ballan wrasse Labrus bergylta

In wild ballan wrasse Labrus bergylta, mass–length relationships were not different between genders, and positive allometry was found in the mixed‐gender population. Male‐biased sexual size dimorphism was significant and the most effective morphometric method for sexing L. bergylta outside of the species spawning window used body mass (M_B in g), total body length (L_T in mm) and Fulton's condition factor (K) as discriminant variables to predict gender with 91% accuracy. The discriminant score (S_D) of a specimen can be calculated as S_D = 0·01 M_B ? 0·016 L_T ? 3·835 K + 6·252 to predict its gender as female or male if S_D is < 1·459 or S_D is > 1·504, respectively. There was a potential trend towards earlier sexual inversion compared to previous studies at comparable latitudes. Sex change is a phenotypically plastic trait under social control in haremic fishes and should be monitored in increasingly exploited L. bergylta.     

Mapping QTL for Omega-3 Content in Hybrid Saline Tilapia

Tilapia is one of most important foodfish species. The low omega-3 to omega-6 fatty acid ratio in freshwater tilapia meat is disadvantageous for human health. Increasing omega-3 content is an important task in breeding to increase the nutritional value of tilapia. However, conventional breeding to increase omega-3 content is difficult and slow. To accelerate the increase of omega-3 through marker-assisted selection (MAS), we conducted QTL mapping for fatty acid contents and profiles in a F₂ family of saline tilapia generated by crossing red tilapia and Mozambique tilapia. The total omega-3 content in F₂ hybrid tilapia was 2.5 ± 1.0 mg/g, higher than that (2.00 mg/g) in freshwater tilapia. Genotyping by sequencing (GBS) technology was used to discover and genotype SNP markers, and microsatellites were also genotyped. We constructed a linkage map with 784 markers (151 microsatellites and 633 SNPs). The linkage map was 2076.7 cM long and consisted of 22 linkage groups. Significant and suggestive QTL for total lipid content were mapped on six linkage groups (LG3, -4, -6, -8, -13, and -15) and explained 5.8–8.3% of the phenotypic variance. QTL for omega-3 fatty acids were located on four LGs (LG11, -18, -19, and -20) and explained 5.0 to 7.5% of the phenotypic variance. Our data suggest that the total lipid and omega-3 fatty acid content were determined by multiple genes in tilapia. The markers flanking the QTL for omega-3 fatty acids can be used in MAS to accelerate the genetic improvements of these traits in salt-tolerant tilapia.     

Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

To facilitate marker assisted selection, there is an urgent need to construct a saturated genetic map of upland cotton (Gossypium hirsutum L.). Four types of markers including SSR, SRAP, morphological marker, and intron targeted intron–exon splice junction (IT-ISJ) marker were used to construct a linkage map with 270 F_2:7 recombinant inbred lines derived from an upland cotton cross (T586 × Yumian 1). A total of 7,508 SSR, 740 IT-ISJ and 384 SRAP primer pairs/combinations were used to screen for polymorphism between the two mapping parents, and the average polymorphisms of three types of molecular markers represented 6.8, 6.6 and 7.0%, respectively. The polymorphic primer pairs/combinations and morphological markers were used to genotype 270 recombinant inbred lines, and a map including 604 loci (509 SSR, 58 IT-ISJ, 29 SRAP and 8 morphological loci) and 60 linkage groups was constructed. The map spanned 3,140.9 cM with an average interval of 5.2 cM between two markers, approximately accounting for 70.6% of the cotton genome. Fifty-four of 60 linkage groups were ordered into 26 chromosomes. Multiple QTL mapping was used to identify QTL for fiber quality traits in five environments, and thirteen QTL were detected. These QTL included four for fiber length (FL), two for fiber strength (FS), two for fiber fineness (FF), three for fiber length uniformity (FU), and two for fiber elongation (FE), respectively. Each QTL explained between 7.4 and 43.1% of phenotypic variance. Five out of thirteen QTL (FL1 and FU1 on chromosome 6, FL2, FU2 and FF1 on chromosome7) were detected in five environments, and they explained more than 20% of the phenotypic variance. Eleven QTL were distributed on A genome, while the other two on D genome.     

Life history of the symbiotically luminous cardinalfish Siphamia tubifer (Perciformes: Apogonidae)

Characteristics of the life history of the coral reef‐dwelling cardinalfish Siphamia tubifer, from Okinawa, Japan, were defined. A paternal mouthbrooder, S. tubifer, is unusual in forming a bioluminescent symbiosis with Photobacterium mandapamensis. The examined S. tubifer (n = 1273) ranged in size from 9·5 to 43·5 mm standard length (L_S), and the minimum size at sexual maturity was 22 mm L_S. The number of S. tubifer associated during the day among the spines of host urchins was 22·9 ± 16·1 (mean ± s.d .; Diadema setosum) and 3·6 ± 3·2 (Echinothrix calamaris). Diet consisted primarily of crustacean zooplankton. Batch fecundity (number of eggs; F_B) was related to L_S by the equations: males (fertilized eggs) F_B = 27·5L_S ? 189·46; females (eggs) F_B = 31·3L_S ? 392·63. Individual mass (M; g) as a function of L_S was described by the equation: . Growth, determined from otolith microstructure analysis, was described with the von Bertalanffy growth function with the following coefficients: L_∞ = 40·8 mm L_S, K = 0·026 day^?1 and t₀ = 23·25 days. Planktonic larval duration was estimated to be 30 days. The age of the oldest examined individual was 240 days. The light organ of S. tubifer, which harbours the symbiotic population of P. mandapamensis, increased linearly in diameter as S. tubifer L_S increased, and the bacterial population increased logarithmically with S. tubifer L_S. These characteristics indicate that once settled, S. tubifer grows quickly, reproduces early and typically survives much less than 1 year in Okinawa. These characteristics are generally similar to other small reef fishes but they indicate that S. tubifer experiences higher mortality.     

Construction of a linkage map of Lentinula edodes (shiitake) with the HEGS (high-efficiency genome scanning) system: use of versatile AFLP and PCR-based gene markers

An improved linkage map of Lentinula edodes (shiitake) was constructed with an HEGS (high-efficiency genome scanning) system. Two hundred twenty-one HEGS-derived amplified fragment length polymorphism (AFLP-H) markers and 21 gene markers were developed and combined with 203 previously developed sequencer-derived AFLP markers (AFLP-S markers) and 3 mating factor loci (A, Bα, and Bβ) to construct a comprehensive linkage analysis. As a result, a novel linkage map with 166 markers including 2 mating factors (A and B), 10 HEGS-derived gene markers, 72 AFLP-H markers, and 82 AFLP-S markers was obtained. Of the total 448 markers, 273 could not be located on a linear map and thus were assigned to linkage groups as accessory markers. The map covers a total length of 1398.4 centimorgans (cM) with an average marker interval distance of 8.4 cM. The map consists of 11 linkage groups (LGs) in agreement with our previous map, and 7 LGs among them were found to contain branched linkages, which may be the result of reciprocal translocations representing dynamic reorganization of the shiitake genome. The previously reported linkage map was improved in terms of number of markers, marker density, linear order of markers, and total map length. Contribution no. 384 of the Tottori Mycological Institute     

Ontogeny of critical and prolonged swimming performance for the larvae of six Australian freshwater fish species

Critical (<30 min) and prolonged (>60 min) swimming speeds in laboratory chambers were determined for larvae of six species of Australian freshwater fishes: trout cod Maccullochella macquariensis, Murray cod Maccullochella peelii, golden perch Macquaria ambigua, silver perch Bidyanus bidyanus, carp gudgeon Hypseleotris spp. and Murray River rainbowfish Melanotaenia fluviatilis. Developmental stage (preflexion, flexion, postflexion and metalarva) better explained swimming ability than did length, size or age (days after hatch). Critical speed increased with larval development, and metalarvae were the fastest swimmers for all species. Maccullochella macquariensis larvae had the highest critical [maximum absolute 46·4 cm s^?1 and 44·6 relative body lengths (L_B) s^?1] and prolonged (maximum 15·4 cm s^?1, 15·6 L_B s^?1) swimming speeds and B. bidyanus larvae the lowest critical (minimum 0·1 cm s^?1, 0·3 L_B s^?1) and prolonged swimming speeds (minimum 1·1 cm s^?1, 1·0 L_B s^?1). Prolonged swimming trials determined that the larvae of some species could not swim for 60 min at any speed, whereas the larvae of the best swimming species, M. macquariensis, could swim for 60 min at 44% of the critical speed. The swimming performance of species with precocial life‐history strategies, with well‐developed larvae at hatch, was comparatively better and potentially had greater ability to influence their dispersal by actively swimming than species with altricial life‐history strategies, with poorly developed larvae at hatch.     

A Consensus Microsatellite-Based Linkage Map for the Hermaphroditic Bay Scallop (Argopecten irradians) and Its Application in Size-Related QTL Analysis

Bay scallop (Argopecten irradians) is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color) markers were mapped to 16 linkage groups (LGs), which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13∶1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL), shell height (SH), shell width (SW) and total weight (TW) were measured for quantitative trait loci (QTL) analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively) were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH) was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS) in bay scallop.     

Quantitative trait loci that harbor genes regulating muscle size in (MRL/MPJ x SJL/J) F(2) mice

The genetic mechanisms that determine muscle size have not been elucidated, even though it is a key musculoskeletal parameter that reflects muscle strength. In this study, we performed a high-density genome-wide scan using 633 (MRL/MPJ × SJL/J) F₂ intercross 7-week-old mice to identify quantitative trait loci (QTL) involved in the determination of muscle size. Significant QTL were identified for muscle size and body length. Muscle size (adjusted by body length) QTL were identified on chromosomes 7, 9, 11, 14 (two QTL) and 17, which together explained 19.2% of phenotypic variance in F₂ mice, while body length QTL were located on chromosome 2 (two QTL), 9, 11 and 17 which accounted for 28.3% of phenotypic variance in F₂ mice. Three significant epistatic interactions between different QTL positions from muscle size and body length were identified (P <0.01) on chromosomes 2, 9, 14 and 17, which explained 16.1% of the variance in F₂ mice. Electronic Publication     

Redescription of Chlorophthalmus corniger,a senior synonym of Chlorophthalmus bicornis (Family: Chlorophthalmidae)

Chlorophthalmus corniger is redescribed on the basis of recently collected specimens. The species is redefined as a species of Chlorophthalmus with the lower jaw terminating in a distinctly projecting horizontal plate with strong, spine‐like processes directed forward from the plate's corners; body silvery grey, with numerous minute black spots and traces of broad darker crossbars; base of anterior dorsal fin spines and distal parts of dorsal fins black; adipose fin tiny with numerous black spots; caudal fin black; 3·5 scales above lateral line; three rows of cheek scales; head very large, 34·3–40·1% standard length (L_S); eye large, 29·8–40·8% head length (L_H); pectoral fin long, extending to beyond dorsal fin base, 21·7–26·2% L_S. Chlorophthalmus bicornis is a junior synonym of C. corniger based on the examination of the type series of both species. It is confined to the northern half of the Indian Ocean, reliably recorded from Somalia and the Gulf of Aden to southern Java, Indonesia, at depths between 200 and 500 m. A lectotype and three paralectotypes were designated for C. corniger. DNA barcodes for Indian species of Chlorophthalmus were generated.     

Balitora eddsi,a new species of hillstream loach (Ostariophysi: Balitoridae) from Nepal

A new species of hillstream loach Balitora eddsi is described from the Karnali River drainage in south‐western Nepal. The new species is distinguished from all its congeners by possessing the following combination of characters: six to seven unbranched pectoral‐fin rays, pelvic‐fin length 12–14% standard length (L_S), dorsal surface without circular or irregular shaped dark blotches, snout pointed, median lobe between anterior rostral barbels pointed posteriorly, dorsal‐fin origin posterior to pelvic‐fin origin, lateral line scales 66–67, caudal peduncle length 22–23·2% L_S, caudal peduncle depth 4·1–4·2 times its length.     

QTL for body weight,morphometric traits and stress response in European sea bass Dicentrarchus labrax

Natural mating and mass spawning in the European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) complicate genetic studies and the implementation of selective breeding schemes. We utilized a two‐step experimental design for detecting QTL in mass‐spawning species: 2122 offspring from natural mating between 57 parents (22 males, 34 females and one missing) phenotyped for body weight, eight morphometric traits and cortisol levels, had been previously assigned to parents based on genotypes of 31 DNA microsatellite markers. Five large full‐sib families (five sires and two dams) were selected from the offspring (570 animals), which were genotyped with 67 additional markers. A new genetic map was compiled, specific to our population, but based on the previously published map. QTL mapping was performed with two methods: half‐sib regression analysis (paternal and maternal) and variance component analysis accounting for all family relationships. Two significant QTL were found for body weight on linkage group 4 and 6, six significant QTL for morphometric traits on linkage groups 1B, 4, 6, 7, 15 and 23 and three suggestive QTL for stress response on linkage groups 3, 14 and 23. The QTL explained between 8% and 38% of phenotypic variance. The results are the first step towards identifying genes involved in economically important traits like body weight and stress response in European sea bass.     

QTL analysis of agronomic traits in recombinant inbred lines of sunflower under partial irrigation

The objective of the present research was to map QTLs associated with agronomic traits such as days from sowing to flowering, plant height, yield and leaf-related traits in a population of recombinant inbred lines (RILs) of sunflower (Helianthus annuus). Two field experiments were conducted with well-irrigated and partially irrigated conditions in randomized complete block design with three replications. A map with 304 AFLP and 191 SSR markers with a mean density of 1 marker per 3.7 cM was used to identify QTLs related to the studied traits. The difference among RILs was significant for all studied traits in both conditions. Three to seven QTLs were found for each studied trait in both conditions. The percentage of phenotypic variance (R ²) explained by QTLs ranged from 4 to 49%. Three to six QTLs were found for each yield-related trait in both conditions. The most important QTL for grain yield per plant on linkage group 13 (GYP-P-13-1) under partial-irrigated condition controls 49% of phenotypic variance (R ²). The most important QTL for 1,000-grain weight (TGW-P-11-1) was identified on linkage group 11. Favorable alleles for this QTL come from RHA266. The major QTL for days from sowing to flowering (DSF-P-14-1) were observed on linkage group 14 and explained 38% of the phenotypic variance. The positive alleles for this QTL come from RHA266. The major QTL for HD (HD-P-13-1) was also identified on linkage group 13 and explained 37% of the phenotypic variance. Both parents (PAC2 and RHA266) contributed to QTLs controlling leaf-related traits in both conditions. Common QTL for leaf area at flowering (LAF-P-12-1, LAF-W-12-1) was detected in linkage group 12. The results emphasise the importance of the role of linkage groups 2, 10 and 13 for studied traits. Genomic regions on the linkage groups 9 and 12 are specific for QTLs of leaf-related traits in sunflower.     

Description of Triplophysa luochengensis sp. nov. (Teleostei: Nemacheilidae) from a karst cave in Guangxi,China

A new cave‐dwelling fish Triplophysa luochengensis is described based on specimens collected from a karst cave in Guangxi Zhuang Autonomous Region, China, that is interconnected to the Hongshui River drainage. The species can be distinguished from its congeners by a combination of characters: eyes degenerated, anal fin with six branched rays, caudal fin with 16–17 branched rays, pectoral‐fin length 72·4–95·8% of the distance between pectoral‐fin origin and pelvic‐fin origin, lateral head length 26·2–28·2% of standard length (L_S), eye diameter 7·5–8·6 of L_S, body covered by sparse scales, lateral line complete and 7–8 pre‐operculo‐mandibular pores. Dark pigments irregularly present on dorsum of head, dorsum and flank.     

Dietary analysis of the herbivorous hemiramphid Hyporhamphus regularis ardelio: an isotopic approach

The stable isotope values for a range of size classes of Hyporhamphus regularis ardelio from Moreton Bay, south‐east Australia were determined. There was a positive linear relationship between δ¹³C and standard length (L_S)(δ¹³C = 0·034 L_S ? 16·23; r² = 0·78). δ¹³C ranged from ?8·48 to ?17·29‰ with the smallest size class (50 mm L_S) being on average 1·04‰ enriched with respect to that of zooplankton (Temora turbinata) and 7·97‰ depleted compared to Zostera capricorni. δ¹³C was positively correlated with L_S(P < 0·01)(more enriched with increasing L_S) with those fish of the largest size class (225 mm L_S) being 9·86 and 0·84‰ enriched than T. turbinata and Z. capricorni, respectively. There was no detectable trend in δ¹⁵N values with L_S(P > 0·01) with δ¹⁵N, ranging from 9·18 to 11·00‰. Fish of all size classes were on average 2·32 and 7·63‰ more enriched than zooplankton and seagrass, respectively. Carbon isotope data indicate that H. r. ardelio commence life as carnivores and change to a diet in which seagrass is the primary carbon source. The dependence on animal matter, however, is always present. Due to the low percentage of nitrogen in Z. capricorni(2·5%) compared to zooplankton (9·1%) it appears that nitrogen from zooplankton is necessary throughout their life history with the carbon requirements for these fish coming chiefly from Z. capricorni.     

Development and ossification of the feeding apparatus in the larvae of two co‐occurring species of kob (Sciaenidae), Argyrosomus japonicus and Argyrosomus inodorus,in South Africa

The teeth of the oral jaws of two sympatric species of Argyrosomus, Argyrosomus japonicus and Argyrosomus inodorus, found along the South African coast developed first on the premaxilla and then on the dentary of the lower jaw. Teeth were observed on the premaxilla of A. inodorus [head length (L_H) = 1·0 mm; notochord length (L_N) = 2·7 mm] at a smaller size than in A. japonicus (L_H = 1·2 mm; L_N = 4·7 mm). The ventral elements of the gill arches (hypo‐ and basibranchials) were not ossified by the end of preflexion. The fifth ceratobranchial began ossifying and possessed pharyngeal teeth by 1·2 mm L_H (L_N = 4·7 mm) in A. japonicus and 1·1 mm L_H (L_N = 3·2 mm) in A. inodorus. To complement the osteological data, stomach contents were also analysed as a proxy for feeding apparatus functionality. Prey were first present in the stomach of A. japonicus at 1·2 mm L_H (L_N = 4·7 mm) and only 22% of the stomachs contained no prey suggesting that A. japonicus is already actively foraging by preflexion. In comparison, 83% of the stomachs of A. inodorus contained no prey and a single prey item was present in the largest examined specimen (L_H = 1·6 mm; L_N = 5·4 mm). Elements of the feeding apparatus begin to ossify early during ontogeny. While the overall pattern of ossification is similar between the two species, A. japonicus may be able to begin feeding at smaller head lengths relative to A. inodorus in their nursery habitats.     

Empirical standard mass equation for Salmo marmoratus

Total length (L_T) (range 24–1000 mm; mean ±s.e . = 170·21 ± 0·36 mm) and mass (W) (range 0·10–9590 g; mean ±s.e . = 76·03 ± 0·87 g) of 36 460 specimens of marble trout Salmo marmoratus were used to compute a standard mass (W_s) equation for this species by means of the empirical percentile (EmP) method. The EmP W_s equation calculated was: log₁₀W_s = ?5·208 + 3·202 log₁₀L_T? 0·046 (log₁₀L_T)² (L_T range 90–570 mm) and it is valid throughout the species' area of distribution across Europe.