Iranian Scientific Fisheries Journal

fa مقاله علمی – پژوهشی:‌ تفاوت‌‌های ریختی و الگوی رشد بین جمعیت‌‌های مختلف کپور معمولی در ایران Phenotype and growth trend differences in varied populations of common carp in Iran ژنتيك و اصلاح نژاد ژنتيك و اصلاح نژاد پژوهشي Research از مهم‌ترین اقدامات آغازین در تشکیل یک بانک ژن زنده، تشکیل جمعیت مرجع با تنوع ژنتیکی و ریختی گسترده است. در این مطالعه، تفاوت‌‌های ریختی بین چهار جمعیت مختلف کپور معمولی (شمال ایران، جنوب ایران، چینی و کاسپی) در اولین بانک ژن زنده این ماهی درکشور بررسی شد که در ابتدا تمایز ژنتیکی آنها با نشانگر SNP بر پایه توالی‌‌یابی کل ژنوم از یکدیگر مشخص شد. رشد طولی و وزنی و ارتفاع و قطر بدن در طول دو سال در جمعیت‌‌ها بررسی شد. نتایج نشان‌دهنده آن بود که به دلیل فاصله ژنتیکی کم بین جمعیت‌‌های شمال و جنوب ایران و جمعیت تاتا، لایه‌‌بندی جمعیتی بین این جمعیت‌‌های این مناطق وجود نداشت و نمونه‌‌ها از نظر ژنتیکی یکنواخت بودند. جمعیت‌‌های چینی و کاسپی، تفاوت ژنتیکی را با سه جمعیت دیگر نشان دادند. نتایج آزمون‌های آنالیز واریانس یک‌طرفه و چندطرفه نشان داد که نوع جمعیت، جنسیت، زمان و اثرات تعاملی آنها بر تغییرات تمام اندازه‌گیری‌های بدنی اثرات معنی‌‌دار دارد (05/0> p). بیشترین ارتفاع بدن در همه فصول متعلق به کپور جنوب ایران بود که با شکل بشقابی آن مطابقت دارد که نتیجه انتخاب چندین ساله تکثیرکنندگان این جمعیت‌‌ها در خوزستان با توجه به بازارپسندی آن است. پس از کپور جنوب ایران، کپور تاتا نیز دارای ارتفاع و قطر بیشتر بدن نسبت به دو جمعیت دیگر (شمال ایران و چینی) است. همچنین کمترین تغییرات در مقدار ارتفاع بدن متعلق به کپور جنوب ایران و پس از آن تاتا بود که با یکدست بودن ریخت این جمعیت‌‌ها مطابقت داشت. در همه جمعیت‌‌ها، اندازه‌‌های بدنی در جنس ماده بزرگتر از جنس نر بود به‌‌ویژه بیشترین تفاوت در وزن و طول بدن مشاهده گردید. ارتباط بین طول کل و وزن در سه جمعیت تاتا مجارستان، چینی و شمال ایران کاملاً مشهود بود، اما در جمعیت جنوب ایران، داده‌‌ها بیانگر پراکندگی بودند و کمترین ارتباط بین طول و وزن در این جمعیت مشاهده شد. روند رشد در تاتا بهتر از شمال ایران و چینی است. با توجه به وجود تفاوت‌های ریختی و رشدی بین جمعیت‌ها، باید برنامه‌های انتخاب ژنتیکی با رویکرد بهینه‌سازی و استفاده از تنوع ژنتیکی موجود صورت پذیرد. Introduction Common carp is one of the most widely cultured freshwater fish species worldwide, having been introduced to all continents except Antarctica over the past two centuries. There are different populations of common carp, which can be morphologically distinguished, including Cyprinus carpio carpio, C. c. haematopterus, C. c. viridiviolaceus, and C. c. aralensis, each native to various regions such as Ponto-Caspian, the far East, northern Vietnam, and central Asia. These populations inhabit diverse environments due to their genetic diversity and adaptation capabilities. These genetic diversities lead to distinct phenotypic modifications, including variations in growth rate, body color, scale pattern, body shape, temperature, and hypoxia. One crucial initial step in establishing a living gene bank is to form a reference population that exhibits wide genetic and morphological diversity. Genetic diversity enables species to adapt to changing environments, and it provides a valuable source of individuals and genes for selective breeding programs in aquaculture, which can help meet production and consumer demands for fish strains. Knowledge of the population structure and genetic variation of existing strains/ populations is necessary for fish management and conservation, and many molecular markers and genetic tools have been used to evaluate the genetic diversity of common carp populations. In this study, we investigated the morphological differences between various common carp populations collected for the country's first live gene bank. These populations included Hungarian TATA (Cyprinus carpio carpio), China-originated (C. c. haematopterus), North Iran, and South Iran populations, all of which were initially genetically differentiated from one another using whole-genome single-nucleotide polymorphism (SNP) markers. Methodology The populations (South Iran, North Iran, TATA, and China-originated carp) were cultured under the same conditions in earthen ponds with the flow-through system at the South Iran Aquaculture Research Institute (SIARI). Each individual was tagged with a Passive Integrated Transponder (PIT) tag, and the phenotypic indices, including the length and weight growth, body height, and body width, were investigated in the populations over two years. Samples for genomic analysis were taken from the caudal fin and preserved in ethanol. Genomic DNA was isolated with a Denazist Kit (S-1033 GBS, Iran) with some modifications to the protocol. The purity of DNA was quantified and assessed with a NanoDrop Microvolume Spectrophotometer (Hercuvan Lab System Nano.300, Malaysia), while DNA integrity was evaluated through 1% agarose gel electrophoresis. After ensuring the quality of the extracted DNA, the samples were sent to BGI China for sequencing. The 2100 Bioanalyzer system was used for quality control of DNA samples. FastQC was employed to check the quality of the raw sequence data from high-throughput sequencing pipelines, and data editing was performed using Trimmomatic software version 0.35. The BWA-MEM algorithm was used to align the sequence reads against a large reference genome for alignment. The pairwise population genetic differentiation index (FST) was used to differentiate the populations. It is important to note that the Caspian-sea common carp population was collected for the gene bank but not included in the breeding stage, and no morphological data was recorded for it. This population was included in this study solely to assess the differentiation and genetic identity of the breeding populations from North and South Iran and to understand its relationship with the breeding populations. Results The results indicated no population stratification among the North Iran, South Iran, and TATA populations, as evidenced by the low genetic distance between them. The samples from these regions were relatively genetically uniform. However, the populations from China and the Caspian Sea showed genetic differences compared to the other three populations (Fig 1). Figureure 1: Tagging and recording the phenotypic and biometric indices of selected individuals After the south Iran carp population, the TATA population exhibited the highest average body weight, length, and width at the end of the period. The distribution of individuals based on weight growth in all three populations is skewed, resulting from the selection of superior individuals after one year of breeding. However, at the end of the breeding period, the distribution in the Hungarian and North Iran populations is normal, displaying no skewness or kurtosis. In contrast, the China-originated and south Iran show skewness and kurtosis in one direction (Fig. 2). Figure 2: Cluster analysis of Common carp population originated from five different region Wild refers to Caspian carp Results from one-way ANOVA and Multivariate analysis of variance tests revealed that factors such as population, sex, time, and their interaction influenced all body measurements. The highest body height across all seasons belonged to the South Iran carp, which is consistent with their plate shape. This is likely a result of several years of selective breeding by farmers in Khuzestan, emphasizing marketability. The TATA carp also exhibited greater body height and width than the northern and Chinese populations. Additionally, the South Iran population had the lowest variance in body height, followed by the TATA population, which aligns with the morphological uniformity observed in these groups. In all populations, males exhibited larger body sizes than females, with the most significant differences noted in terms of body weight and length. The TATA, China-originated, and North Iran populations showed a clear correlation between total length and weight. In contrast, the South Iran population demonstrated more dispersion, showing the lowest correlation between length and weight. Notably, the growth trend in the TATA population was superior to that of the Northern Iran and China-originated carp. Discussion and conclusion The common carp populations in Iran originated from Hungary approximately 70 years ago. Since genetic diversity is the origin of morphological differences between populations, the morphological characteristics of these populations closely resemble those of the Hungarian TATA population. This similarity in body shape (characterized by high body height and a plate-like shape) in these populations can be attributed to their genetic background. The genetic differences observed between different common carp populations in Iran highlight the importance of maintaining these diverse populations in live gene banks. Except for the South Iran population, the TATA population showed satisfactory growth compared to other populations. The variations in growth between these populations point to genetic influences, suggesting potential for improvement through selective breeding. Additionally, sex has been identified as a factor that affects body measurements, which should be taken into account in selection and breeding programs. Weight and length are traits that exhibit both genetic and phenotypic correlations. Nielsen et al. (2010) observed a relatively high heritability for weight, length, and survival during the six months leading up to harvest in common carp, indicating that selective breeding for growth and survival is likely to be successful. Given the substantially estimated within-population additive genetic variance for weight, there is considerable potential for creating a synthetic population with a strong genetic foundation. This could be utilized to establish a selective breeding program for common carp at SIARI. The findings of this study are valuable for developing genetic selection programs for common carp and enhancing the potential for utilizing this species' genetic resources. This research can serve as a foundation for future studies and practical applications in various aspects of common carp aquaculture. In aquaculture programs, it is essential to prioritize the maintenance and increase of genetic diversity within different common carp populations. Conflict of Interest The authors declare that there are no conflicts of interest. Acknowledgment We would like to express our gratitude to the Khuzestan Governorate, Iran's Vice-Presidency for Science, Technology, and Knowledge-Based Economy Affairs, and the Iranian Fisheries Research Institute (IFSRI) for their financial support of common carp breeding project. This study is part of project No. 124-74-12-033-98043-981235. Cyprinus carpio, تنوع ژنتیکی, رشد, به‌‌گزینی Cyprinus carpio, Genetic diversity, growth, Selection 1 17 http://isfj.ir/browse.php?a_code=A-10-2139-2&slc_lang=fa&sid=1 Ayeh Sadat Sadr آیه سادات صدر AyehSadr@gmail.com 100319475328460040312 100319475328460040312 No Agricultural Research, Education and Extension Organization سازمان تحقیقات، آموزش و ترویج کشاورزی Samira Nazemroaya سمیرا ناظم رعایا samira.nazemroaya@gmail.com 100319475328460040313 100319475328460040313 Yes Agricultural Research, Education and Extension Organization سازمان تحقیقات، آموزش و ترویج کشاورزی Mohammad Youneszadeh Feshalami محمد یونس زاده فشالمی m_yooneszadeh@yahoo.com 100319475328460040314 100319475328460040314 No Agricultural Research, Education and Extension Organization سازمان تحقیقات، آموزش و ترویج کشاورزی Fatemeh Hekmatpour فاطمه حکمت پور hekmatpourf@gmail.com 100319475328460040315 100319475328460040315 No Agricultural Research, Education and Extension Organization سازمان تحقیقات، آموزش و ترویج کشاورزی Hossein Houshmand حسین هوشمند houshmand.hossein@gmail.com 100319475328460040316 100319475328460040316 No Agricultural Research, Education and Extension Organization سازمان تحقیقات، آموزش و ترویج کشاورزی Mina Ahahangarzadeh مینا آهنگرزاده Minaahangarzadeh@gmail.com 100319475328460040317 100319475328460040317 No Agricultural Research, Education and Extension Organization سازمان تحقیقات، آموزش و ترویج کشاورزی Mahdi Golshan مهدی گلشن mahdigolshan@gmail.com 100319475328460040318 100319475328460040318 No Agricultural Research, Education and Extension Organization سازمان تحقیقات، آموزش و ترویج کشاورزی Mahmoud Hafezieh محمود حافظیه 100319475328460040319 100319475328460040319 No Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran مؤسسه تحقیقات علوم شیلاتی کشور، سازمان تحقیقات، آموزش و ترویج کشاورزی، تهران، Mansour Sharifian منصور شریفیان sharif_23@yahoo.com 100319475328460040320 100319475328460040320 No Agricultural Research, Education and Extension Organization سازمان تحقیقات، آموزش و ترویج کشاورزی Elham Jorfi الهام جرفی ejorfi@gmail.com 100319475328460040321 100319475328460040321 No Agricultural Research, Education and Extension Organization سازمان تحقیقات، آموزش و ترویج کشاورزی Farahnaz Kianersi فرحناز کیان ارثی ننادگانی 100319475328460040322 100319475328460040322 No South of Iran Aquaculture Research Institute, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Ahvaz, Iran پژوهشکده آبزی‌پروری جنوب کشور، مؤسسه تحقیقات علوم شیلاتی کشور، سازمان تحقیقات، آموزش و ترویج کشاورزی، اهواز، ایران