Genetic Diversity of a Closed Population of Japanese Black Cattle in Hyogo Prefecture Takeshi HONDA, Tetsuro NOMURA1, Moriyuki FUKUSHIMA2 and Fumio MUKAI Faculty of Agriculture, Kobe University, Nada-ku, Kobe-shi 657-8501, Japan Faculty of Engineering, Kyoto Sangyo University, Kita-ku, Kyoto-shi 603-8555,1 Japan Hyogo Prefectural North Insitute of Agriculture, Wadayama-machi, Hyogo-ken 669-5254,2 Japan (Received March 1, 2001; Accepted June 15, 2001) Abstract The Japanese Black in Hyogo prefecture has been almost closed population. In this paper, genetic diversity of the population was estimated. The materials used were 68,781 animals born in 1955 to 1998 and their pedigree records traced back to the population in 1937 or before. To assess the diversity, three types of parameters were estimated. Founder genome equivalents (Nge) is the most comprehensive parameter, in which all the causes of the reduction of diversity are accounted for. Effective number of founders (Nef) explains the cause of reduced diversity due to unequal contributions of founders. Effective number of non-founders (Nenf) accounts for the diversity reduced by genetic drift accumulated over non-founders generations. Index of genetic diversity (GD) was estimated by GD=1-1/(2Nge). Nge decreased gradually from 26.9 in 1955 and reached 2.2 in 1998. Before 1970, Nenf showed larger values than Nef, but the order was reversed in the later years. Nenf in the recent years was close to Nge. The index GD showed a sharp decline after 1980 and reached 0.78 in 1998. The major cause of the reduced genetic diversity was considered to be the bottleneck effect due to the concentrated use of breeding animals originated from a few founders. Animal Science Journal 72 (5): 378-385, 2001 Key words: Japanese Black, Genetic diversity, Effective number of founders, Genetic contributions, Founder genome equivalents The Japanese Black is one of the domestic beef breeding stock to the whole breed7). To maintain breeds, with about 50,000 to 60,000 reproductive cows such prominent characteristics, the population in registered annually. Since liberalization of beef Hyogo prefecture has been almost completely closed import restriction in 1991, the production of high- to the other populations. Thus, the amount of in- quality beef has received more attention to compete breeding and relationship of the population become with the economical by imported beef. Accordingly, considerably higher, and breeders are concerned about genetic evaluation with best linear unbiased prediction a decay of genetic variability. (BLUP) under animal model was introduced in the The loss of genetic variability in domestic animals same year. Nomura et al.9) reported that both the causes some undesirable phenomena such as inbreed- increasing rate of relationships and decrease of effec- ing depressions, reduced long-term genetic responses, tive population size in the Japanese Black have been and random fluctuation of selection responses. Ge- accelerated after the initiation of BLUP evaluation. netic variability is also essential for the adaptation to Because of the high meat quality, the Japanese unexpected changes of economic and environmental Black population in Hyogo prefecture has drawn spe- conditions, such as change of consumers' preference cial attention since early times. Especially, Mikata and prevalence of a novel disease. region has slaved an important role in supplying The purpose of the present study was to estimate the Corresponding: Fumio MUKAI (fax: +81 (0) 78-803-5801, e-mail: [email protected]) Anim. Sci. J. 72 (5): 378-385, 2001 378 Genetic Diversity of Japanese Black Table 1. Numbers of reproductive bulls and cows born in each year, and the actual number of founders (Nf) amount of the genetic diversity and survey the genetic The ancestors with unknown parents are referred to as structure of the population in Hyogo prefecture in founders, and all of their descendants are to as non- terms of population genetic parameters derived from founders. The population of founders is the base genetic contributions of ancestors. population of pedigree analysis. All the parameters were estimated for the population of registered Materials and Methods animals born in each year from 1955 to 1998. These Pedigree records of breeding stock were kept by populations are referred to as reference populations. Wagyu Registry Association and Hyogo Branch of The numbers of bulls and cows born in each year are Wagyu Registry Association. All the animals are shown in Table 1. Total number of animals in the uniquely identified by the registry numbers assigned reference populations was 68,781. by Wagyu Registry Association. Information availa- The depth of pedigree in each reference population ble for each animal are names and registry numbers of was examined by computing the number of discrete the animal and its parents, and the date and place of generation equivalents (ge)15), which is the expected birth. Although the oldest animal was traced back to number of generations from the base population to the 1871, we used the pedigree data of the animals born reference population if generations proceeded dis- after 1937, from which centralized registry system was cretely. This parameter is obtained by initiated. The data consisted of 90,694 animals. Anim. Sci. J. 72 (5): 378-385, 2001 379 HONDA, NOMURA, FUKUSHIMA and MUKAI sity of the reference population. ge=1/NΣN j=1Σni i=11/2gij, All the causes of the reduction of genetic diversity where nj is the total number of ancestors of animal j in are fully accounted for by founder genome equivalents the reference population, gij is the number of genera- (Nge). This parameter is estimated by tions between animal j and its ancestor i, and N is the number of animals in the reference population15). Nge=1/ΣN i=1ΣN j=1 aij/N2, Genetic diversity in a closed population is decayed by three different causes, i. e. unequal genetic contribu- where aij is additive relationship coefficient between tion of founders, Mendelian sampling in meiosis, and individual i and j. The denominator is the average of the bottleneck effect3). The unequal genetic contribu- full additive relationship matrix A (including recipro- tion is of special importance in a population under cal and diagonal elements)3, 5). artificial selection, because genetic improvement is The third type of effective number of animals, the attained at the expense of reduced contributions of effective number of non-founders (Nenf), accounts genetically inferior founders16). Mendelian sampling only for the effects of Mendelian samplig and bottle- is an inevitable cause for reduction of genetic diversi- necks. This effective number is obtained from the ty, when parents are heterozygotes. Loss of genetic relation3) diversity due to the bottleneck effect will also be important under the intensive use of a few popular 1/ Nge=1/Nef+1/Nenf. (1) sires. According to Lacy4, 5),the amount of genetic diver- To assess the amount of genetic diversity and clarify sity (GD) or expected heterozygosity8) in the reference the relative importance of three causes of the reduc- population relative to the base population is estimated tion, we first estimated three types of effective num- by bers of animals, i. e. effective number of founders, GD=1-1/2Nge. founder genome equivalents, and effective number of non-founders. The effective number of founders The lowest value is estimated at 0.0 when Nge is only (Nef) is estimated by 0.5. Analogously, the genetic diversity estimated by Nef=ΣNi i=1 GD*=1-1/2Nef (Ci/N)2, accounts only for the decay due to unequal contribu- where Nf is the number of founders, N is the number tions of founders3). From equation (1), the differ- of animals in the reference population, and ci is the ence of these two indices of genetic diversity is sum of direct relationships between founder i and GD*-GD=1/2Nenf. animals in the reference population4, 11). In this study, we defined ci/N as genetic contributions of This difference represents the amount of the genetic founder i, so that it can be considered as expected diversity reduced by Mendelian sampling and bottle- frequencies of alleles derived from founder i in the necks, which is theoretically equivalent to the amount reference population. The effective number of of genetic drift accumulated over non-founder founders is affected only by the variation of genetic generations3). contributions among founders. In an extreme case Results and Discussion where all the founders give an exactly same contribu- tion, Nef is equal to the actual number of founders, Nf The information about generations traced back (for Nf in the reference population, see Table 1). from the reference populations to founders can be Since Nef does not take account of the effect of genetic seen in Fig. 1. During the period of 1955 to 1998, drift caused by Mendelian sampling and bottlenecks in the number of discrete generation equivalents in- subsequent generations, it overestimates genetic diver- creased from 3.6 to 7.9, meaning that the average Anim. Sci. J. 72 (5):378-385, 2001 380 Genetic Diversity of Japanese Black Fig. 1. The number of discrete generation equivalents and maximum number of generations traced from population in each year. generation interval was about 10 years in this period. effective number, founder genome equivalents (Nge), Maximum number of generations traced back from gradually decreased from 26.9 in 1955, and reached animals in 1955 and 1998 to the base population were 2.2 in 1998, implying that the genetic diversity in the 7 and 16, respectively. current population would be equivalent to the diversi- Distributions of inbreeding coefficient of each ty in a random mating population derived from only 2 animal and additive relationship coefficient among a -3 non -related founders .