The Genetics and Genomics of Cyprinids Laszlo Orban1,2 And
Total Page：16
File Type：pdf, Size：1020Kb
The Genetics and Genomics of Cyprinids Laszlo Orban1,2 and Qingjiang Wu3 1) Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 2) Department of Biological Sciences, National University of Singapore, Singapore 3) Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China 2 1. Introduction Cyprinids are arguably the most important group of freshwater teleosts. Their most popular representative, the common carp is the most extensively cultivated fish species and perhaps the best known teleost in the world. A number of detailed reviews have been published earlier about the genetics and aquaculture of common carp (see e.g. Balon, 1995; Horvath and Orban, 1995; Gomelsky, 2003; Vandeputte, 2003), some of them discussed these topics in wider context by including results on the related cyprinids as well (see e.g. Hulata, 1995b; 2001; Penman, 2005). This chapter aims to review the history and current status of cyprinid genetics and genomics. Besides describing the state of the art for the tools and approaches available it will also suggest possibilities for future developments. Similarly to the other studies mentioned above, the topic is discussed - with the exception of the section on the resources - by concentrating on the most important species of the group, the common carp. In the resource section the premier model species of teleosts, the zebrafish takes the center stage, due to the fact, that most of the tools of cyprinid genomics were first developed for and applied to that species. Throughout the whole chapter the authors tried to take every opportunity to broaden the topic to comparative aspects of the area by including information about other cyprinids and occasionally other teleost species important for research or aquaculture, whenever it was possible. 3 2. The biology and history of farmed cyprinids 2.1. The taxonomy and physiology of farmed cyprinids Cyprinids are ray-finned teleosts (Actinopterygii class) from the infraclass of Teleostei and the order of Cypriniformes. According to FishBase1 the family of Cyprinidae contains 210 genera and over 2,000 species (Froese and Pauly, 2005). The typical features of the cyprinid body are the following: toothless jaw, pharyngeal teeth in the throat (ideal for characterization), the presence of Weberian organ at the beginning of vertebrate column and the complete lack of spiny rays on the dorsal fin. Cyprinid species naturally occur in wide-ranging habitats in the Northern temperate zone and the tropical regions as well. Most of them are confined to freshwater bodies, only few species are found at estuaries. {For a review on morphological and taxonomic analysis of cyprinid subfamilies and their geographical distribution see Howes (1991)}. Cyprinids exhibit a wide variety of spawning behaviors (Mills, 1991). Some species, such as common carp and goldfish, lay their adhesive eggs onto the vegetation or the bottom. Others drop their pelagic eggs in the stream (grass carp and silver carp) or shed their eggs in gravelly bottom (zebrafish). Due to their wide geographical range and excellent adaptational abilities cyprinids play an important role in the food chain of natural freshwater bodies and in the ponds of commercial fisheries as well. The selected set of most important cyprinid species discussed in this chapter is shown in Table 1. In addition to common carp the so-called “Chinese carp” species (i.e. bighead carp, grass carp and silver carp) are the most important for aquaculture. Additional cyprinids often used in culture (and/or 1 For a list of important and useful websites related to this topic (labeled with bold and italics throughout the text) see Section 10. 4 research) are the following: goldfish, ginbuna, Prussian carp (silver crucian carp or gibel carp), and crucian carp. The list is completed by the striped petfish commonly known as zebrafish. This species, which has become one of the major vertebrate models during the past three decades, also belongs to the family of Cyprinidae and its research provides useful data, especially for the comparative aspects. Additional cyprinid species, such as the black carp (Mylopharyngodon piceus; Richardson 1846), the so-called “Indian major carps”, such as the catla (Catla catla; Hamilton, 1822) the mrigal (Cirrhinus cirrhosus; Bloch, 1795), and the rohu (Labeo rohita; Hamilton, 1822) (Jhingran and Pullin, 1988; Singh and Mittal, 1990) or the tench (Tinca tinca; Linaeus 1758) (Flajshans et al., 1993a; Buchtova et al., 2003) are not being discussed in detail here and they are only referred to occasionally. 2.2. Classical studies on the taxonomy and origin of farmed cyprinids Most experts agree that common carp, as a species seems to have originated from East Asia and apparently split from other members of the Cyprininae subfamily in the middle of the Miocene (Zardoya and Doadrio, 1999). There are however several different hypotheses on the phylogeography of the various phenotypic forms of common carp that exist today. According to Berg (1964) carp originally inhabited a continuous range in Eurasia, which was divided later into Eastern and Western populations during the Pleistocene. Balon’s opinion was entirely different: he postulated that common carp has originated from the area bordered by the draineages of Black, Caspian and Aral seas and later dispersed to the East and West (Balon, 1995). On the basis of morphological differences four different subspecies of common carp have been proposed by Kirpichnikov (1967): European- Transcaucasian carp (Cyprinus carpio carpio), Central Asian carp (C.c. aralensis), East Asian carp (C. c. haematopterus) and South Asian carp (C. c. viridiviolaceus). Wu (1977) accepted only three subspecies: C.c. carpio, C.c. 5 haematopterus and C. c. rubrofuscus2 with different zoogeographical ranges: C. c. carpio had the widest range from Danube River to Volga River and with additional populations in the Xinjiang Uygur Autonomous Region of China; C.c. haematopterus originated from the North of Nanling Mountains in China; whereas C.c. rubrofuscus from the South of Nanling Mountains. Balon (1995) listed only two subspecies: C.c. carpio and C.c. haematopterus, which show distinctly different morphological characteristics as described earlier by Svetovidov (1933) and questioned the existence of the others. There is no data on the exact origin of carassids in the peer-reviewed literature. The ancestors of this group are thought to have originated from the Far East. There are two different species discussed in the chapter from the Carassius genus: namely Carassius carassius, and C. auratus. The second species is divided into three subspecies: the goldfish (C. a. auratus), the Prussian carp or silver crucian carp (C. a. gibelio3) and the ginbuna (C. a. langsdorfii). The goldfish has more phenotypic forms than any other ornamental aquarium species (Smartt and Bundell, 1996). The Prussian carp and ginbuna differ from the rest of the members of the group as they are both triploid and gynogenetic. The former is widely distributed in China, Russia and large part of Europe, whereas the latter is only found in Japan. According to FishBase (Froese and Pauly, 2005) zebrafish is native to several South Asian countries. On the basis of original collection data the geographic range of the species has been reconstructed as follows: “from 2 Cyprinus carpio rubrofuscus is also mentioned in the literature as C. c. viridiviolaceus and C. c. nigroauratus. FishBase classifies this taxon on the basis of morphological data as a separate species (C. rubrofuscus), however on the basis of molecular data we refer to it as a subspecies in this chapter. 3 FishBase refers to it as a separate species (C. gibelio). 6 Pakistan in the west to Myanmar (Burma) in the east and from Nepal in the north to the Indian state of Karnataka in the south” (Engeszer et al., 2007). 2.3. The history of cyprinid aquaculture 2.3.1. The aquaculture of common carp Ancient Chinese documents show that cultivation of common carp started around 4000 years ago. Pond fish culture in China began in the Shang Dynasty, 12th century BC, with common carp as the main cultivated species. Common carp has been reared on the large scale in China since the Zhou Dynasty, 5th –2nd century BC. The book of Fan Li from 460 BC (“Fish culture classic”) is the earliest written document about fish cultivation. It stimulated prosperous development of freshwater fish cultivation in China at the end of Zhou Dynasty, had a positive influence on common carp culture of South Asia and later to that of Europe as well. During the Han Dynasty (from 206 BC to 220 AD) common carp cultivation reached its prosperous period. During that period, common carp remained to be cultured as the primary species, but not only in ponds, in open water bodies as well. Records from the age of the Han Dynasty, such as “History Record” by Shima, show that common carp was cultured in waters spanning hundreds of hectares. During the Tang Dynasty (618-907 AD) common carp culture was banned because the Chinese name of common carp (“Li”) was same as the emperor’s family name, thus common carp was regarded as a symbol of their family. The legislation banned people from sacrificing and selling common carp and captured individuals had to be returned into the river. It is unknown to us when exactly common carp was first cultured Japan, but according to Chiba and colleagues (1966) a pond was built in Kawachi Province in 31 BC. Although a Chinese book of the Western Jin Dynasty (4th century) mentioned carp with various colors, systematic koi carp breeding is 7 thought to have begun only around the 17th century in Japan. Monks were probably responsible for some of the early carp introductions to South-East Asia (Steffens, 1999). According to the prevalent view (see e.g. Günther, 1868; Chiba et al., 1966; Vooren, 1972) the ancestor of European domestic carp was the Asian common carp which was transported from Asia to Europe during the ancient Greek and Roman times.