Genetic evidence for the mating system and reproductive success of black sea bream (Acanthopagrus schlegelii)

Swinging back from the brink? Polygamous mating strategies revealed for an iconic threatened freshwater fish

Catastrophic fish death events are increasing in frequency and severity globally. A series of major recent fish deaths in the semi-arid lower Darling-Baaka river system (LDBR) of Australia are emblematic of these issues with tens of millions of native fish perishing. In 2018-2019 there was a major death event for Australia's largest freshwater fish, Murray cod (Maccullochella peelii). To aid the recovery and guide restoration activities of local Murray cod populations, it is essential to gather information on the mating strategies and effective population size following the fish death event. After the fish deaths, we collected larvae during the 2020 and 2021 breeding seasons and used single nucleotide polymorphisms (SNPs) to provide insight mating strategies and to estimate effective population size. Larvae were detected in both years along the entire length of the LDBR. Sixteen percent of the inferred breeding individuals were found to contribute to multiple pairings, confirming a complex and polygamous mating system. A high frequency of polygamy was evident both within and between years with 100 % polygamy identified among parents that produced offspring in both 2020 and 2021 and 95 % polygamy identified among parents involved in multiple spawning events within years. Post-larval Murray cod samples collected between 2016 and 2021 were co-analysed to further inform kinship patterns. Again, monogamy was rare with no confirmed cases of the same male-female pair contributing to multiple breeding events within or between seasons. Effective population size based on Murray cod collected after the fish death event was estimated at 721.6 (CI 471-1486), though this has likely declined following a subsequent catastrophic fish death event in the LDBR in March 2023. Our data provide insight into the variability of Murray cod mating strategies, and we anticipate that this knowledge will assist in planning conservation actions to ultimately help recover a species in crisis.

Microsatellite Genome-Wide Database Development for the Commercial Blackhead Seabream (Acanthopagrus schlegelii)

Simple sequence repeats (SSRs), the markers with the highest polymorphism and co-dominance degrees, offer a crucial genetic research resource. Limited SSR markers in blackhead seabream have been reported. The availability of the blackhead seabream genome assembly provided the opportunity to carry out genome-wide identification for all microsatellite markers, and bioinformatic analyses open the way for developing a microsatellite genome-wide database in blackhead seabream. In this study, a total of 412,381 SSRs were identified in the 688.08 Mb genome by Krait software. Whole-genome sequences (10×) of 42 samples were aligned against the reference genome and genotyped using the HipSTR tools by comparing and counting repeat number variation across the SSR loci. A total of 156,086 SSRs with a 2–4 bp repeat were genotyped by HipSTR tools, which accounted for 55.78% of the 2–4 bp SSRs in the reference genome. High accuracy of genotyping was observed by comparing HipSTR tools and PCR amplification. A set of 109,131 loci with a number of alleles ≥ 3 and with a number of genotyped individuals ≥ 6 were reserved to constitute the polymorphic SSR database. Fifty-one polymorphic SSR loci were identified through PCR amplification. This strategy to develop polymorphic SSR markers not only obtained a large set of polymorphic SSRs but also eliminated the need for laborious experimental screening. SSR markers developed in this study may facilitate blackhead seabream research, which lays a certain foundation for further gene tagging and genetic linkage analysis, such as marker-assisted selection, genetic mapping, as well as comparative genomic analysis.

Spawning time of black sea bream Acanthopagrus schlegelii, related to underwater photoperiodism in oyster farms

The embryonic development times, spawning timing and hatching rates of the black sea bream Acanthopagrus schlegelii were examined to investigate the potential effect of seawater temperature, tides and photoperiod on the reproductive rhythm of this species in Hiroshima Bay, Japan. Low temperatures decreased hatching rates and extended the hatching time, and the minimum temperature threshold for hatching was 15°C. Back-calculated spawning times indicated that the peak of spawning occurred just before sunset and the reduction in diurnal light intensity around the oyster rafts acted as a trigger for spawning. In contrast, no correlation was found between spawning rhythms and tidal cycle. The results highlight the important role of oyster farms in the reproductive cycle and population dynamics of A. schlegelii in Hiroshima Bay, the main spawning ground for this species in Japan. The study findings provide insights for the sustainable management of this important sparid species.

Characteristics of the Mating Behavior of Domesticated Geese from Anser cygnoides and Anser anser

Mating behavior is a critically important component of poultry reproduction. Here, a total of 135 geese were selected, specifically, Sichuan white geese (Anser cygnoides), Zhedong white geese (Anser cygnoides), and Hungarian geese (Anser anser) (300-day-old), and the mating behavior was monitored daily from 6:00 a.m. to 6:00 p.m. during the 20-day observation period. The results showed that the mating process included mounting, female cooperation, and successful copulation. Overall, the three breeds preferred mating on land. More than thirty percent of the mating time was primarily concentrated from 4:00 p.m. to 6:00 p.m. in domesticated geese from Anser cygnoides, the corresponding values for Sichuan white geese and Zhedong white geese were 32.0% and 33.3%, respectively. The mating of the Hungarian geese usually took place in the morning. In addition, the frequency of successful copulation of Sichuan white geese and Zhedong white geese were 2.31 and 1.94 times per day, significantly greater than that of Hungarian geese (0.89 times). Furthermore, a significant positive correlation between successful copulation and laying rates (r = 0.985) or fertilization rates (r = 0.992) was observed in Hungarian geese. Taken together, the mating behaviors among the different breeds were mainly reflected in time preference and successful copulation frequency.

Genetic Evaluation of Black Sea Bream (Acanthopagrus schlegelii) Stock Enhancement in the South China Sea Based on Microsatellite DNA Markers

This is the first genetic evaluation of hatchery-based stock enhancement of black sea bream (Acanthopagrus schlegelii) in the South China Sea after a two-year monitoring period. In this study, microsatellite DNA markers were used to calculate the contribution rate and analyze genetic changes before and after stock enhancement. Two out of one hundred and sixty nine individuals from three recaptured populations were assigned to broodstock with a contribution rate of 1.18%, revealing that the hatchery-released juvenile fish could survive in the natural environment and had a positive effect on population replenishment in wild black sea bream abundance. However, we found that the release population had the lowest genetic diversity and significant genetic differentiation from other populations. In addition, genetic diversity detected in the recaptured population was lower than that in the wild population, and their genetic differentiation reached a significant level. Our results suggested that releasing cultured black sea bream juveniles with low genetic quality might be genetically harmful for the maintenance of wild genotypes. Therefore, it is necessary to assess the genetic variation of the hatchery population before implementing a stock enhancement and establish a long-term evaluation for monitoring the genetic effect caused by releasing this fish species.

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean H_o = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.