Search

The Pacific white shrimp or white leg shrimp, Penaeus vannamei, is native to the tropical coastal regions of Central and South America. It is one of the three major shrimp species with high production worldwide. It was brought from Hawaii, USA, in 1988 and introduced into China. It has been widely promoted and cultivated due to its adaptability to the environment, fast growth rate, and suitability for high-density industrial farming. As of 2022, China's total production of P. vannamei reached 2.09 million tons, accounting for > 90% of the country's total shrimp farming production. It has become one of the pillar industries in China's aquaculture sector.With the continuous expansion of aquaculture, diseases are becoming increasingly severe. Among them, acute hepatopancreatic necrosis disease (AHPND) hinders the development of the global shrimp farming industry and causes catastrophic economic losses. After infection, most shrimp show hepatopancreatic enlargement, which appears pale white or light yellow. In the later stages of infection, some diseased shrimp may exhibit atrophy of the hepatopancreas, appearing reddish-brown and blackened, with a hardened texture. Within 20–30 d after infection, death can occur, with a mortality rate of up to 90%. As of 2021, the economic losses caused by this disease to the major P. vannamei farming areas (China, Malaysia, Thailand, Vietnam, and Mexico) have exceeded 43 billion US dollars. Cultivating novel P. vannamei germplasm with AHPND resistance is an effective way to solve AHPND.Recently, domestic researchers have established independent shrimp breeding systems and cultivated 12 novel P. vannamei strains, such as "Hai Xing Nong No.2", "Ren Hai No.1", and "Zheng Jin Yang No.1". These varieties mainly target traits such as growth, resistance to white spot syndrome virus, farming survival rate, and temperature, salinity, and ammonia nitrogen tolerance. However, no reports of novel varieties specifically targeting AHPND resistance are available. Growth traits are essential economic traits in the genetic breeding of aquatic animals. Among the 12 novel P. vannamei varieties in China, 11 have excellent traits related to growth. Evaluating the genetic relationship between growth and AHPND resistance in the core breeding population of P. vannamei is important for fully utilizing existing high-quality germplasm and breeding novel varieties with composite traits and AHPND resistance.Genetic parameters reflect the genetic variation of target traits in a breeding population and are important references for breeding decisions. Due to the complex genetic background of existing P. vannamei germplasm resources in China, genetic parameters are influenced considerably by the tested population, infection methods, and other factors. Before breeding, stable infection tests must be conducted on the base population and obtain accurate parameters.This study used two independently bred P. vannamei strains as research objects to test their growth and AHPND resistance. Among them, 40 families were selected for high resistance (20 individuals per family, total 800 experimental individuals), and 30 families were selected for fast growth (32 individuals per family, total 960 experimental individuals). The test was conducted at P70–P90 by feeding with VpAHPND quantitative oral infection. Feeding with toxic bait was stopped after 50% of the experimental individuals died. The genetic heritability and correlation of the weight, individual survival time after VpAHPND infection, and half-lethal survival rate of the two strains were evaluated using individual animal and male and female threshold models. The results showed that the weight heritability estimate of the highly resistant strain was 0.599±0.120, indicating a high level of genetic heritability. The heritability estimates of survival time and half-lethal survival rate were 0.240±0.072 and 0.173±0.051, respectively, indicating a moderate to low level of genetic heritability, and all significantly different from 0 (P < 0.01). The weight heritability estimate of the fast-growth strain was 0.266±0.082, indicating a low level of genetic heritability. The heritability estimates of survival time and half-lethal survival rate were 0.374± 0.096 and 0.257±0.048, respectively, indicating a moderate level of genetic heritability, and all significantly different from 0 (P < 0.01). The genetic correlation between weight and AHPND resistance traits (survival time and half-lethal survival rate) in both strains showed a low positive correlation (0.061–0.235), and no significant difference was observed from 0 (P > 0.05). The genetic correlation between survival time and half-lethal survival rate in both strains was highly positively correlated, with estimates of 0.997±0.129 and 0.967±0.044, respectively. The results indicate that growth and AHPND resistance can be included as selection indicators in the comprehensive selection index for breeding and seed production in the actual breeding process. Under limited conditions, the infection program can be simplified, and the half-lethal survival rate can be used as the AHPND resistance indicator for the breeding population. This study provides a primary reference for utilizing existing germplasm resources to develop high-quality P. vannamei strains for growth and AHPND resistance breeding.

The Pacific white shrimp Penaeus vannamei is one of the most productive shrimp species in China and the world. Domestic demand for P. vannamei has increased annually because of its fast growth, easy breeding, strong resistance to stress and disease, and high meat yield. The primary challenge in the development of the shrimp industry is seed rearing. The demand for broodstocks of P. vannamei in China is as high as 1, 000, 000 pairs per year, and the total weight of shrimp seedlings exceeds 1.3 trillion. China needs to import 300, 000 pairs of P. vannamei every year. The cost of each pair of P. vannamei is approximately 200 US＄, thus equating to hundreds of millions of US＄ in total. During the production of P. vannamei, the spawning frequency varies greatly among female shrimp. Cultivating high-fecundity P. vannamei through genetic improvement is an effective way to reduce the cost of seedling farms and improve economic benefits.To further study the molecular mechanisms of fecundity differences in female P. vannamei, the ovarian histology and expression of four candidate genes in populations with high- and low-fecundity were analyzed in this study. Before the experiment, the 7-month-old parent shrimp of P. vannamei were fed a commercial parent shrimp fortified diet, a maturation promoting diet, and squid for nutritional enhancement. After one month of promoting maturity, the unilateral eyestalk of female shrimp was cut using forceps, and next-generation family construction began after 15–20 days of recovery. The spawning frequency of 439 female shrimp in the 30-day production cycle was calculated and used to indicate fecundity. Those with a spawning frequency of 0 were included in the low-fecundity group, while those with a spawning frequency of > 3 were included in the high-fecundity group. The ovarian development of P. vannamei was divided into four stages (proliferation, small growth, large growth, and maturation) according to the color, size, and shape of the ovaries. In the high-fecundity group, the ovaries exhibited development up to stageⅣ, indicating their attainment of maturity. In the low-fecundity group, ovarian development was limited to stageⅢ, with progression to stageⅣ proving difficult. Ovarian tissues from the same part of female shrimp of stageⅠ–Ⅳ in the high-fecundity group and stageⅠ–Ⅲ in the low-fecundity group were taken and immediately immersed in tissue fixative for paraffin sectioning. The research team previously identified candidate genes related to fecundity in genomic regions undergoing selective sweep in isolated populations. These included thioredoxin 2 (TRX2), partitioning-defective 3 (PARD3), phospholipase Cβ4 (PLCβ4), and arginine-glutamate acid dipeptide repeats (RERE), which play important roles in oocyte maturation, cell proliferation, and early development in other species. qRT-PCR was used to analyze and compare their expression in the ovary and eyestalk tissues of high- and low-fecundity females at different stages of ovarian development.The results of paraffin section showed that the ovarian development of the low-fecundity group was slower than that of the high-fecundity group. In the high-fecundity group, stageⅠ ovaries primarily consisted of oogonia and oocytes during the early phase of yolk formation, with the emergence of small spherical yolk granules. StageⅠ ovaries in the low-fecundity group primarily consisted of oogonia, with no observable yolk granule formation. StageⅡ ovaries in the high-fecundity group were mainly composed of oocytes with vitelline formation, accompanied by a notable augmentation in both the size and number of yolk granules. StageⅡ ovaries in the low-fecundity group primarily comprised oocytes in the early phase of vitelline formation with yolk granules beginning to form. StageⅢ ovaries in the high-fecundity group consisted mainly of oocytes during the late phase of yolk formation. Many spherical yolk granules were formed in the cytoplasm, and cortical rods began to appear, although the lengths of the cortical rods were short. StageⅢ ovaries in the low-fecundity group were composed of oocytes during yolk formation. The cytoplasm was full of spherical yolk granules in the absence of cortical rods. In the high-fecundity group, stage Ⅳ ovaries were filled with mature oocytes, large yolk granules filled the entire cytoplasm, and thick cortical rods were formed in the oocytes. qRT-PCR showed that the four genes maintained high expression levels in the mature ovaries of the high-fecundity group. Their expression levels in the ovaries of the high-fecundity group were higher than those in the ovaries of the low-fecundity group in the small and large growth stages. TRX2, PLCβ4, and RERE expression levels were significantly different between the groups (P < 0.05). In eyestalk tissues at different stages, TRX2, PARD3, PLCβ4, and RERE expression levels in the low-fecundity group were higher than those in the high-fecundity group. The results suggest that these four genes may play important roles in the ovarian development of P. vannamei. The expression levels of all four genes in the high-fecundity group were lower than those in the low-fecundity group in eyestalk tissues. However, in ovarian tissues, except for the PARD3 gene in stageⅠ, which was expressed at lower levels in the high-fecundity group than in the low-fecundity group, the expression levels of all four genes in the other stages were higher in the high-fecundity group than those in the low-fecundity group, which is opposite to the expression trend in eyestalk tissues. Therefore, we speculate that these genes also promote cell proliferation, development, and target gene expression in the eyestalks of the low-fecundity group. Their high expression in the eyestalks of the low-fecundity group may enhance the secretion of ovarian inhibitory factors, thereby inhibiting ovarian development. Further research is needed to reveal their functional mechanisms. The above results provide an important reference for the in-depth study of the molecular mechanisms of differences in the fecundity of female P. vannamei.

Penaeus vannamei, also known as white foot shrimp, is globally one of the three high-yield shrimp farming varieties. The wild species is found along the Pacific coast of South America. Since 1988, China has introduced P. vannamei. Due to its strong environmental adaptability, high feed conversion rate, fast growth rate, and high tolerance to ammonia nitrogen and nitrite, it has been widely promoted in aquaculture. By 2021, the aquaculture output of P. vannamei in China reached 1.977 million tons, accounting for approximately 37% of the world's total production, and has extremely high economic value.Growth traits are among the most important economic factors in the production of P. vannamei. With the intensive development of shrimp farming and degradation of germplasm, the white spot syndrome virus (WSSV) is a serious disease faced by the global shrimp industry. The infection can cause symptoms such as reduced food intake, enlarged liver and pancreas, pale red body color, and white spots on the head and chest armor in shrimp, resulting in widespread death.At present, China has cultivated 12 new varieties of P. vannamei, which to some extent alleviates its dependence on imports for high-quality P. vannamei. However, the excellent traits of domestic shrimp species are singular, and cultivating new varieties of P. vannamei with fast growth and strong disease resistance is an urgent demand in the market. Genetic parameter evaluation is the fundamental work of selection breeding. Heritability reflects the genetic variation in traits in the breeding population, which is of great significance in the development of a selection index, prediction of selection response, comparison of selection methods, selection breeding planning, and other breeding processes. There are different degrees of genetic correlation among various quantitative traits of shrimp, and genetic correlation coefficients are important for selecting target traits. The estimation of genetic correlation can be used to develop a comprehensive selection index and breeding program of multiple traits, which can improve the selection efficiency and breed better varieties with multiple traits. The higher the genetic correlation between traits, the better the effect of indirect selection. The estimation of genetic parameters is greatly affected by the test population, breeding management, analysis methods, and other factors. To ensure the accuracy of multi-trait composite breeding for growth and WSSV resistance, accurate evaluation of growth and WSSV resistance needs to be carried out for specific breeding populations. There are two commonly used target traits for measuring WSSV resistance in P. vannamei: individual survival time after infection and half-lethal survival rate (SS50) of families. In practice, measuring the half-lethal survival rate of families is more convenient. However, the correlation between these two traits has not yet been reported.To promote the growth and WSSV resistance of P. vannamei, 59 families (1, 770 individuals) were tested for WSSV infection. We recorded the survival time and individual body length of shrimp after infection and analyzed the mean, standard deviation, maximum and minimum values, and coefficient of variation of half-lethal survival rate and test traits for each line. The heritability and genetic correlation coefficients of growth, survival time, and half-lethal survival rate were calculated. Variance components and genetic parameters for growth and survival traits were estimated using a two-trait animal model and a sire-dam threshold model. The genetic parameters of body length were corrected by including age as a covariate. The genetic parameters of WSSV survival time were corrected by including body length as a covariate. The estimated heritability of body length was medium (0.17±0.05), and the estimated heritabilities of survival time and half-lethal survival rate were medium (0.18±0.05 and 0.14±0.05). Further, the estimated heritabilities of the three traits were significantly different from zero (P < 0.01). The genetic correlation between body length and survival time and that of body length and half-lethal survival rate were low (0.15±0.20 and 0.25±0.22). There were no significant differences between the genetic correlations and zero (P > 0.05). The genetic correlation between survival time and half-lethal survival rate was high (0.96±0.03). There was no significant difference between the genetic correlation and one (P > 0.05). The results showed that a comprehensive selection index of growth and WSSV resistance of P. vannamei can be established to carry out multi-trait composite breeding. In this breeding population, the growth and WSSV resistance of P. vannamei can be combined with multiple traits according to the breeding requirements, and the comprehensive selection index can be formulated by assigning values. In addition, to optimize the breeding of each generation, the half-lethal survival rate of WSSV can be used as an indicator of WSSV resistance. This study provides basic data and theoretical support for breeding varieties of P. vannamei with excellent growth and WSSV resistance.

Litopenaeus vannamei, also known as the Pacific white shrimp or white foot shrimp, is a member of the Crustacea, Decapoda, Palaemonidae, and Litopenaeus families. This species is mainly distributed on the Mexican and Pacific coasts of South America. Owing to its excellent immune characteristics, L. vannamei is currently one of the most important economic shrimp species in China.In the aquaculture process and under natural environmental conditions, low dissolved oxygen (DO) condition or even hypoxia frequently occurs. Under high-density culture operations, acute hypoxia is one of the major factors affecting the survival rate of shrimp and the quality of aquaculture water, causing not only a large number of shrimp deaths in the short term but also water decay and fermentation, increased turbidity, and other phenomena. The genetic improvement of L. vannamei, as well as the screening and breeding of exceptionally tolerant species under low DO conditions, are crucial to the sustainable development of the shrimp industry. Global selective breeding efforts based on quantitative genetics to improve genetic progress in L. vannamei have been extensive, and the main targeted traits were growth, survival, disease resistance, and stress tolerance. Few studies have been conducted on the evaluation of genetic parameters and screening of strains for hypoxic tolerance traits in L. vannamei; in particular, the genetic parameters and cytological characteristics of key tissues of L. vannamei under short-term highly lethal DO levels (0.3–0.5 mg/L) have not been reported.In this study, we used two strains of L. vannamei, GK (a strain with high disease resistance) and K (a strain with fast growth characteristics), each with a total of 6 560 shrimp from 41 families, to count survival traits at highly lethal DO levels, analyze differences in hypoxia tolerance traits between strains and within families of the same strain, and evaluate genetic parameters. Individual gill, muscle, and hepatopancreas tissues from families with significantly different tolerance levels were histologically investigated and compared at the cellular level. The results showed that there was a significant difference (P < 0.05) in semi-lethal survival (SS50) between families within both the GK and K strains when overall semi-lethality was reached under hypoxic environmental conditions of 0.3 mg/L, with SS50 values of 49.30% for GK and 42.52% for K. The coefficients of variation for survival times of families within each strain were 60% and 45% for GK and K, respectively. Using the threshold trait animal model, the genetic parameters were estimated to be between 0.345±0.031 and 0.378±0.029 using the survival status of the individual at semi-lethal levels as the observed value (1 for survival and 0 for death), and the heritability was between 0.219±0.031 and 0.237±0.029 following transformation on a continuously varying scale of observed values, indicating a moderate level of heritability. Moreover, the gill, muscle, and hepatopancreas tissues of the hypoxia-tolerant and hypoxia-sensitive families in the GK strain exhibited varying degrees of damage and different degrees of variations in the physiological characteristics of resistance among different families. This may be related to the resistance tolerance strength of different GK families. In contrast to the gill, muscle, and hepatopancreas tissues of the control shrimp, the equivalent tissues of shrimp from tolerant and sensitive families showed different degrees of changes following stress. The gill lumen of the filaments of the experimental group from sensitive families increased, the number of blood cells increased, the structure of the epithelial layer was gradually destroyed or even disintegrated, the vacuolation of the hepatopancreas was severe, the lumen of the ducts became irregularly deformed, and the muscle tissue muscle bundle interval widened with a certain degree of deformation. These results suggested that there was abundant genetic variation in the tolerance traits of L. vannamei at highly lethal DO levels and that this species was amendable to selective breeding practices. This study provides a reference and basis for the selection and breeding of hypoxia-tolerant traits in L. vannamei.

Selecting shrimp strains that perform well on a plant-based diet holds promise for solving the fishmeal (FM) shortage issue, with genetic improvement of feed efficiency (FE) being a key focus. This study compared a plant-based (fishmeal-free) diet with a 25% FM diet for the Pacific whiteleg shrimp (Penaeus vannamei) to determine whether the FE-related traits, including residual feed intake (RFI), average daily weight gain (ADG), and daily feed intake (DFI), exhibit diet-specific genetic variations and genotype-by-diet (genotype × diet) interactions. Results showed that RFI was significantly higher under the plant-based diet treatment compared to the FM-based diet treatment (0.0049 g/d vs. –0.0045 g/d, p < 0.001), while ADG was notably lower (0.043 g/d vs. 0.110 g/d, p < 0.001), indicating that a plant-based diet may lead to reduced yields and impact the profitability of shrimp culture. In the case of being unable to estimate common environmental effects, the heritability estimates of RFI under the plant-based and FM-based diets were 0.743 ± 0.157 and 0.440 ± 0.125, respectively, and those of ADG and DFI ranged from 0.314 ± 0.121 to 0.947 ± 0.158. Genetic correlations between diets for RFI and DFI were 0.646 ± 0.162 and 0.549 ± 0.163, respectively, suggesting a degree of genotype × diet interactions. In contrast, the genetic correlation between diets for ADG was only 0.296 ± 0.259, indicating a strong genotype × diet interaction. These findings highlight the importance of considering selective breeding for improved feed efficiency in a plant-based diet environment.

The current study aimed to provide a precise assessment of the genetic parameters associated with growth and white spot syndrome virus (WSSV) resistance traits in Pacific white shrimp (Litopenaeus vannamei). This was achieved through a controlled WSSV challenge assay and the analysis of phenotypic values of five traits: body weight (BW), overall length (OL), body length (BL), tail length (TL), and survival hour post-infection (HPI). The analysis included test data from a total of 1017 individuals belonging to 20 families, of which 293 individuals underwent whole-genome resequencing, resulting in 18,137,179 high-quality SNP loci being obtained. Three methods, including pedigree-based best linear unbiased prediction (pBLUP), genomic best linear unbiased prediction (GBLUP), and single-step genomic BLUP (ssGBLUP) were utilized. Compared to the pBLUP model, the heritability of growth-related traits obtained from GBLUP and ssGBLUP was lower, whereas the heritability of WSSV resistance was higher. Both the GBLUP and ssGBLUP models significantly enhanced prediction accuracy. Specifically, the GBLUP model improved the prediction accuracy of BW, OL, BL, TL, and HPI by 4.77%, 21.93%, 19.73%, 19.34%, and 63.44%, respectively. Similarly, the ssGBLUP model improved prediction accuracy by 10.07%, 25.44%, 25.72%, 19.34%, and 122.58%, respectively. The WSSV resistance trait demonstrated the most substantial enhancement using both genomic prediction models, followed by body size traits (e.g., OL, BL, and TL), with BW showing the least improvement. Furthermore, the choice of models minimally impacted the assessment of genetic and phenotypic correlations. Genetic correlations among growth traits ranged from 0.767 to 0.999 across models, indicating high levels of positive correlations. Genetic correlations between growth and WSSV resistance traits ranged from (−0.198) to (−0.019), indicating low levels of negative correlations. This study assured significant advantages of the GBLUP and ssGBLUP models over the pBLUP model in the genetic parameter estimation of growth and WSSV resistance in L. vannamei, providing a foundation for further breeding programs.

The Pacific whiteleg shrimp (Penaeus vannamei) is a highly significant species in shrimp aquaculture. In the production of shrimp larvae, noticeable variations in the reproductive capacity among female individuals have been observed. Some females experience slow gonadal development, resulting in the inability to spawn, while others undergo multiple maturations and contribute to the majority of larval supply. Despite numerous studies that have been conducted on the regulatory mechanisms of ovarian development in shrimp, the factors contributing to the differences in reproductive capacity among females remain unclear. To elucidate the underlying mechanisms, this study examined the differences in the ovarian characteristics between high and low reproductive bulks at different maturity stages, focusing on the cellular and molecular levels. Transmission electron microscopy analysis revealed that the abundance of the endoplasmic reticulum, ribosomes, mitochondria, and mitochondrial cristae in oocytes of high reproductive bulk was significantly higher than that of the low reproductive bulk in the early stages of ovarian maturation (stages I and II). As the ovaries progressed to late-stage maturation (stages III and IV), differences in the internal structures of oocytes between females with different reproductive capacities gradually diminished. Transcriptome analysis identified differentially expressed genes (DEGs) related to the mitochondria between two groups, suggesting that energy production processes might play a crucial role in the observed variations in ovary development. The expression levels of the ETS homology factor (EHF) and PRDI-BF1 and RIZ homology domain containing 9 (PRDM9), which were significantly different between the two groups, were compared using qRT-PCR in individuals at different stages of ovarian maturation. The results showed a significantly higher expression of the EHF gene in the ovaries of high reproductive bulk at the II and IV maturity stages compared to the low reproductive bulk, while almost no expression was detected in the eyestalk tissue of the high reproductive bulk. The PRDM9 gene was exclusively expressed in ovarian tissue, with significantly higher expression in the ovaries of the high reproductive bulk at the four maturity stages compared to the low reproductive bulk. Fluorescence in situ hybridization further compared the expression patterns of EHF and PRDM9 in the ovaries of individuals with different fertility levels, with both genes showing stronger positive signals in the high reproductive bulk at the four ovarian stages. These findings not only contribute to our understanding of the regulatory mechanisms involved in shrimp ovarian development, but also provide valuable insights for the cultivation of new varieties aimed at improving shrimp fecundity.

To explore the performance differences among offspring obtained by the intra- and inter-strain crosses, strain A with outstanding WSSV resistance and strain B with outstanding growth of Litopenaeus vannamei were used to construct four experimental groups in a complete diallel cross. 27 growth-related phenotypic traits and WSSV resistance represented by the surviving hours post-infection were obtained via the growth and the virus challenge test. Mixed linear model along with physical pedigree were utilized to calculate the least squares means, correlations, heritability and heterosis. The results showed that crossbreeding can realize character complementation of advantage strain. The performance of WSSV resistance was ranked AA> BA> AB> BB, and the reciprocal crosses performed significantly better than intra-strain group BB. Most growth-related traits in two reciprocal cross groups were also significantly better than those in AA group. Comparisons between the two reciprocal crosses showed that BA cross was better than AB in terms of WSSV resistance and growth. Heterosis of WSSV resistance in BA cross was 5.74∼10.18% greater than that in AB, meanwhile the absolute weight gain rate of BA cross was 4.83% higher than that of AB. The heritability estimates of body length and body weight were 0.0278 and 0.339, both of which reached medium level. The genetic and phenotypic correlations among growth-related traits were from 0.36 to 0.99 and 0.32 to 0.99, respectively. In term of WSSV resistance, the heritability estimate was 0.135 ± 0.082. The genetic and phenotypic correlations between WSSV resistance and growth-related traits were from − 0.034 to − 0.573 and − 0.001 to − 0.202, respectively. The results showed that hybrid offspring obtained by crossing female parents with outstanding WSSV resistance and male parents with outstanding growth culminated in a superior heterosis in both traits. This study provides basic reference data for L. vannamei breeding of new strains that are disease resistant and fast-growing.

The relationship between inbreeding and traits of disease resistance in shrimp has not been studied comprehensively. To explore the effect of inbreeding on white spot syndrome virus (WSSV) resistance in Fenneropenaeus chinensis, we established F. chinensis “Huanghai No. 5” populations with different inbreeding coefficients. We infected F. chinensis individuals with WSSV to compare WSSV-resistance between five inbred groups and a control group. Survival time, survival rate, distribution of deaths, and cumulative mortality rate were analyzed. A mixed linear model was established based on the acquired data. The viral load in muscle tissue of F. chinensis of 12 families from the five inbred groups and the control group was determined at different time points via real-time PCR. The average survival and longest survival time of the inbred groups were lower than those of the control group, and the coefficient of variation was universally greater than that of the control group. The least squares means of survival time of the five inbred groups (F0.1325, F0.25, F0.3125, F0.375, F0.5) were 118.96 115.14, 124.58, 123.97, and 101.34 h, respectively, which were 10.28%, 13.16%, 6.04%, 6.5%, and 23.57% lower than that of the control group. Further, when the inbreeding coefficient increased by 10%, WSSV infection survival time was changed by − 7.76%, − 5.26%, − 1.93%, − 1.73%, and − 4.71% for the five inbred groups, respectively. Thus, the results indicated that inbreeding enhanced the susceptibility of F. chinensis to WSSV infection, and the resistance of F. chinensis to WSSV declined as the inbreeding coefficient values increased, consequently, resulting in greater population dispersion, intensified differentiation, and instability of resistant phenotypes. In conclusion, we elucidated the effect of inbreeding on F. chinensis resistance to WSSV infection and established a theoretical basis to conduct further research in the future.

Penaeusvannamei is the most important economic shrimp in the world. Many selective breeding programs are carried out to improve its production and performance traits. Although significant differences in the reproductive ability of female P. vannamei under artificial breeding conditions have been reported, the genome-wide adaption of the reproductive ability of domesticated female P. vannamei is less investigated. In this study, whole-genome analysis was performed along with pooled DNA sequencing on two fecundity separated bulks, high fecundity bulk (HB), and low fecundity bulk (LB). Each bulk contained 30 individuals from 3 commercial populations. A sequencing depth of >30× was achieved for each bulk, leading to the identification of 625,181 and 629,748 single nucleotide polymorphisms (SNPs) in HB and LB, respectively. Fixation index (Fst) combined with p ratio allowed for the identification of 145 selective sweep regions, with a sequence length of 14.5 Mb, accounting for 0.59% of the genome. Among the 145 selective sweep regions, a total of 64,046 SNPs were identified, and further verification was performed by genotyping 50 candidate SNPs on 60 samples from the offspring of the three populations. Furthermore, 121 genes were screened from the sweep regions. GO annotation and KEGG enrichment analyses showed that partial genes were essential for fecundity regulation. This study provides important information for in-depth investigation of genomic characteristics for long-term selective breeding on the fecundity of female P. vannamei and will also be important for genome-assisted breeding of P. vannamei in the future.

Abstract Fenneropenaeus chinensis is one of the most important aquaculture species in China. Research on its genomic and genetic structure not only helps us comprehend the genetic basis of complex economic traits, but also offers theoretical guidance in selective breeding. In the present study, a genome survey sequencing was performed to generate a rough reference genome utilized for groping preliminary genome characteristics and facilitate linkage and quantitative trait locus (QTL) mapping. Linkage mapping was conducted using a reduced-representation sequencing method 2b-RAD. In total, 36,762 SNPs were genotyped from 273 progenies in a mapping family, and a high-resolution linkage map was constructed. The consensus map contained 12,884 markers and spanned 5257.81 cM with an average marker interval of 0.41 cM, which was the first high-resolution genetic map in F. chinensis to our knowledge. QTL mapping and association analysis were carried out in 29 characters including body size, sex and disease resistance. 87 significant QTLs were detected in several traits and they were also evaluated by association analysis. Results of this study provide us valuable suggestions in genetic improvement and breeding of new varieties and also lay a basic foundation for further application of cloning of economic genes in selective breeding program and marker-assisted selection.

Using pooled DNA genotyping to estimate the proportional contributions from multiple families in a pooled sample is of particular interest for selective breeding in aquaculture. We compared different pooled libraries with separate 2b-RAD sequencing of Litopenaeus vannamei individuals to assess the effect of different population structures (different numbers of individuals and families) on pooled DNA sequencing, the accuracy of parent sequencing of the DNA pools and the effect of SNP numbers on pooled DNA sequencing. We demonstrated that small pooled DNA genotyping of up to 53 individuals by 2b-RAD sequencing could provide a highly accurate assessment of population allele frequencies. The accuracy increased as the number of individuals and families increased. The allele frequencies of the parents from each pool were highly correlated with those of the pools or the corresponding individuals in the pool. We chose 500-28,000 SNPs to test the effect of SNP number on the accuracy of pooled sequencing, and no linear relationship was found between them. When the SNP number was fixed, increasing the number of individuals in the mixed pool resulted in higher accuracy of each pooled genotyping. Our data confirmed that pooled DNA genotyping by 2b-RAD sequencing could achieve higher accuracy than that of individual-based genotyping. The results will provide important information for shrimp breeding programs.

In order to screen the candidate genes of Fenneropenaeus chinensis related to low-temperature tolerance, this research takes juvenile prawns of F. chinensis (P40) in low temperature stress group (4°C) and normal temperature group (18°C) as experimental materials. The results showed that a total of 127,939 Unigenes with average length of 1,190 bp were obtained by assembly, of which 46% were annotated in the Nr database. A total of 1,698 differentially expressed genes were screened by differential gene expression analysis, of which 920 genes showed up-regulated expression and 778 genes showed down-regulated expression. Both GO and KEGG enrichment analysis revealed that differentially expressed genes were enriched in spliceosomes, ribosomes, bile secretion, ABC transport pathways, and cellular nitrogen compound synthesis. A further in-depth analysis obtained 8 genes that may be associated with low-temperature traits of F. chinensis. Five of them displayed up-regulated expression, including ATP-binding cassette protein C, acid ceramidase, glutathione transferase, C-type lectin and heat shock protein HSP70. The remaining three genes, γ-butyl betaine hydroxylase, β-hexosaminidase A and long chain fatty acid-CoA ligase displayed down-regulated expression. Eight differentially expressed genes were randomly selected and the real time RT-PCR verification showed that their expression levels were consistent with the sequencing results, demonstrating the accuracy of the sequencing results. The results of this study provide basic data for revealing the molecular mechanisms of F. chinensis in response to low temperature stress and the molecular assisted breeding of F. chinensis in low temperature.

A multi-trait selective breeding program of Macrobrachium rosenbergii was initiated in China in 2015. In this program, the M. rosenbergii resources were widely collected from four countries, the origin of the founders was verified with 16 microsatellites and the pedigree was reconstructed, and the optimum contribution selection was used to make the mating design. In this study, we evaluated the genetic parameters and selection response for the harvest body weight (HBW) of M. rosenbergii after being communally reared for 95-109 days. The data were collected from two generations that comprised 25,212 progenies from 150 sires and 198 dams. The residual maximum-likelihood methodology was employed to evaluate the variance components, by fitting an animal model. The accuracy of estimated breeding values increased by 0.38% after pedigree reconstruction using microsatellite markers. The estimated heritability (h2) for HBW was moderate (0.212 ± 0.049) and the common environmental coefficient (c2) was low (0.063 ± 0.017) when all the data were used for the analysis. Within generations, h2 was moderate to high (0.198 ± 0.080 to 0.338 ± 0.049). c2 could only be estimated in G1, which was 0.055 ± 0.030. The average HBW of males was significantly larger than that of females (P < 0.01). h2 estimated for female HBWs were higher than that for males within generations, while h2 estimated for female HBWs were lower than that for males across generations. But they were not significantly different (P > 0.05). The genetic correlations between sexes were moderate to high within each generation (0.529 to 0.763). Two methods were used to estimate the realized response. One method was calculated from the differences between the least squares means of the selected population HBW and that of control population HBW, which was 14.01%. The other method was calculated from the differences between the EBVs of the selected population HBW and that of control population HBW, which was 11.52%. The predicted responses derived from two sets of genetic parameters acquired from within- and across- generation datasets were 11.68% and 10.67%, respectively. The present study provides valuable information for breeding programs of M. rosenbergii.

Studying wheat phenology can greatly enhance our understanding of how wheat growth responds to climate change, and guide us to reasonably confront its influence. However, comprehensive global-scale wheat phenology–climate analysis is still lacking. In this study, we extracted the wheat harvest date (WHD) from 1981–2014 from satellite data using threshold-, logistic-, and shape-based methods. Then, we analyzed the effects of heat and drought stress on WHD based on gridded daily temperature and monthly drought data (the Palmer drought severity index (PDSI) and the standardized precipitation evapotranspiration index (SPEI)) over global wheat-growing areas. The results show that WHD was generally delayed from the low to mid latitudes. With respect to variation trends, we detected a significant advancement of WHD in 32.1% of the world’s wheat-growing areas since 1981, with an average changing rate of −0.25 days/yr. A significant negative correlation was identified between WHD and the prior three months’ normal-growing-degree-days across 50.4% of the study region, which implies that greater preseason effective temperature accumulation may cause WHD to occur earlier. Meanwhile, WHD was also found to be significantly and negatively correlated with the prior three months’ extreme-growing-degree-days across only 9.6% of the study region (mainly located in northern South Asia and north Central-West Asia). The effects of extreme heat stress were weaker than those of normal thermal conditions. When extreme drought (measured by PDSI/SPEI) occurred in the current month, in the month prior to WHD, and in the second month prior to WHD, it forced WHD to advance by about 9.0/8.1 days, 13.8/12.2 days, and 10.8/5.3 days compared to normal conditions, respectively. In conclusion, we highlight the effects that heat and drought stress have on advancing wheat harvest timing, which should be a research focus under future climate change.

Regarding the practical farming of Litopenaeus vannamei, the deterioration of water quality from intensive culture systems and environmental pollution is a common but troublesome problem in the cultivation of this species. The toxicities that result from deteriorating water quality, such as that from ammonia stress, have lethal effects on juvenile shrimp and can increase their susceptibility to pathogens. The toxicity of ammonia plays an important role in the frequently high mortality during the early stage on shrimp farms. However, little information is available regarding the genetic parameters of the ammonia tolerance of juveniles in the early stage, but this information is necessary to understand the potential for the genetic improvement of this trait. Considering the euryhalinity of L. vannamei and the fact that low salinity can increase the toxicity of ammonia stress, we estimated the heritability of ammonia tolerance in juveniles in 30‰ (normal) and 5‰ (low) salinity in this study using the survival time (ST) at individual level and the survival status at the half-lethal time (SS50) at the family level. In the normal and low salinity conditions and for the merged data, the heritability estimates of the ST (0.784±0.070, 0.575±0.068, and 0.517±0.058, respectively) and SS50 (0.402±0.061, 0.216±0.050, and 0.264±0.050, respectively) were all significantly greater than zero, which indicates that the ammonia-tolerance of shrimp can be greatly improved. So it might provide an alternative method to reduce mortality, help to enhance resistance to pathogens and reduce the occurrence of infectious diseases. The significant positive genetic correlation between ST and body length suggested that ammonia is more toxic to shrimp in the early stage. The medium-strength genetic correlations of the ST and SS50 between the two environments (0.394±0.097 and 0.377±0.098, respectively) indicate a strong genotype-by-environment (G×E) interaction for ammonia tolerance between the different salinity levels. Therefore, salinity-specific breeding programs for ammonia tolerance in shrimp should be purposefully implemented.

In this study, genetic parameters were obtained for growth and cold tolerance of 99 Fenneropenaeus chinensis juvenile families by means of indoor artificial cooling (starting from 14°C, 2°C/d). A linear mixed model was fitted to estimate variance components using the ASReml software package. Heritabilities estimated for body weight (BW) and body length (BL) of F. chinensis juveniles were 0.078 ± 0.124 and 0.131 ± 0.133, respectively. The estimates of heritability were low in magnitude for both traits. The differences between the heritabilities estimated for the two growth traits were not significant with each other, and the heritabilities were not significantly different from zero (P > 0.05). The phenotypic and genetic correlation coefficients between BW and BL were as high as 0.9408 ± 0.0040 and 0.9562 ± 0.0551, respectively, and both were significantly different from zero (P < 0.01). The heritabilities of temperature at death (TAD) and cooling degree hours (CDH) were 0.265 ± 0.091 and 0.077 ± 0.058, respectively. The heritability estimates for TAD was moderate and significantly different from zero (P < 0.01). The correlation analysis indicated that the phenotypic correlation coefficient between TAD and CDH was -0.5470 ± 0.0174, and the genetic correlation coefficient was -0.6707 ± 0.3635. In the analysis of growth traits and cold tolerance traits, the values of phenotypic correlation coefficient were floating between -0.1055 and 0.1098, both were significantly different from zero (P < 0.05), while the genetic correlation had a larger range (0.0526 ~ 0.9914), and all were not significantly different from zero (P > 0.05). In this study, there was a low correlation between growth and cold tolerance traits, indicating that growth traits and cold tolerance traits should be considered collectively in the breeding program of shrimp.

The rapid and accurate estimation of wheat production at a regional scale is crucial for national food security and sustainable agricultural development. This study developed a new gross primary productivity (GPP) estimation model (denoted as the [ACPM]), based on the effects of light, heat, soil moisture, and nitrogen content (N) on the light-use efficiency of winter wheat. The ACPM model used the quantic additivity of the environmental factors to improve the minimum form or multiple multiplication form in the previous model and thus characterized the joint effects of heat, soil moisture, and N on crop photosynthesis performance. The key parameters (i.e., light) were determined from the photosynthetically active radiation product of the Himawari-8 sensor and the fraction of photosynthetically active radiation product of Moderate Resolution Imaging Spectroradiometer (MODIS). The heat was determined from the land temperature products of MODIS. The soil moisture was obtained from the inversion using a visible and shortwave infrared drought index (VSDI), whereas the N stress of winter wheat was detected using the newly developed modified ratio vegetation index (MRVI), which could accurately obtain the spatiotemporal distribution of the leaf chlorophyll content of winter wheat. The ACPM and two other previous models (named the GPP1 and GPP2 models) were applied on the Himawari-8 and MODIS images in Hengshui City. The evaluation results, based on the ground measurement, indicated that the ACPM models exhibited the best estimate of dry aboveground biomass (DAM) and the wheat yield in Hengshui City, with errors of