In Situ Conservation

Few major crops were domesticated in Japan. Most of Japan's cultigens were introduced initially from China and Korea, and subsequently from other regions. One major crop which could have been domesticated in Japan is the azuki bean, Vigna angularis var. angularis. The fact that today Vigna angularis consists of a wild/weed/crop complex17 is one reason to think that this crop could have been domesticated in Japan.

Recent research at the NIAR has focused on the population structure to be found in this crop complex from different parts of Japan.18 This has highlighted four types of population: wild, weedy, cultivated and complex. Complex populations consist of a mixture of morphological types. It was found that these complex populations have the most genetic variation and are thus the most suitable for in situ conservation and long term monitoring (Table 12.2).19 This research has also found that the present day center of diversity of Vigna angularis in Japan are the prefectures surrounding Osaka, where weedy

Table 12.2. Analysis of genetic diversity in different populations of the Vigna angularis complex19


Genetic diversityb

















2346 0.399


a: Type of population. Complex populations consist of a variety of different plant types; b: Genetic diversity was measured using Jaccard's dissimilarity coefficient; c: Number of individuals in each group.

and complex populations are most frequently found (Fig. 12.4).20

Detailed population level analysis is useful to help elucidate evolutionary pathways and, based on DNA polymorphism, weedy azuki appears to usually have evolved from wild azuki rather than being a hybrid between wild and cultivated azuki or an escape from culti-vation.19 Genebank managers' role in in situ conservation is to facilitate research and monitoring which can help policy makers determine what measures are necessary to efficiently protect genetic resources.


In 1958 the late Dr. H. I. Oka, then of the National Institute of Genetics, Mishima, Japan, was collecting rice in different parts of Thailand. Along a forest trail near Sukothai, Dr. Oka and Thai counterpart scientists found the wild rice O. officinalis. Seeds collected from this population were taken to Japan and several years later a sample was sent to the International Rice Research Institute, the Philippines, for research and conservation. For almost 20 years this accession was conserved before entomologists evaluating wild rices for insect resistance found this population from Thailand to be resistant to brown planthopper, green leafhopper and zigzag leafhopper.21

O. officinalis has a different genome from rice, and producing hybrids with rice is difficult. However, in 1984, because it had useful traits, hybrids with elite rice lines were produced using embryo rescue techniques. Subsequent backcrossing to rice resulted in lines with improved resistance to insects and high yield. These improved lines were tested in international trials in the late 1980s. In Vietnam, where brown planthopper is a serious pest, three of these lines with O. officinalis insect-resistant genes were selected for release to farmers. These three lines were named MTL 98, MTL 103 and MTL 105 in Vietnam.22

From originally being collected to finally providing useful genes to the farmer, more than 30 years had passed. During that time the O. officinalis accession had been multiplied, preserved, distributed and evaluated before finally being used.23

Sumatra in 1974 by Dr. A. T. Perez and collaborators. This upland variety grew to 1300 meter high and was "highly diseased" and had "high sterility" according to the collecting notes of Dr. Perez. Thus it is not surprising that when Indonesian and Japanese scientists visited the area in 1988 they did not find Silewah.24 Two years later, when germplasm collectors visited the village where Silewah was originally collected, Silewah was remembered by one villager but he said it was no longer grown (D. A. Vaughan, 1990, collecting notes)

Cold tolerance/ resistance is a very important trait in areas of high altitude. Cold tolerance is a complex trait since, depending on the location, cold weather may adversely affect rice at any stage. At the International Rice Research Institute (IRRI) 24,158 accessions were screened for cold tolerance. From these, only eleven accessions were selected as cold tolerant varieties.25 These germplasm accessions were subsequently re-evaluated in Japan and Korea. In Hokkaido it was found that Silewah was one of the most tolerant varieties at the booting stage.26 Silewah, a tropical japonica variety, was crossed with a japonica breeding line, Hokkai 241, and indica variety IR38 at IRRI.

After four years of selection, cold tolerant breeding lines were tested in international trials. In Japan, Norin PL8, with genes from Silewah, has been registered under the Seed and Seedling Law of Japan as an important cold tolerant breeding line for temperate and northern areas such as Hokkaido. This example highlights both how evaluation of seemingly unpromising landraces can reveal useful traits, and also the continual replacement (erosion) of varieties in centers of diversity.

Fundamental Genetic Resources Research as the Foundation of Comprehensive Rice Genome Analysis

Three areas of fundamental rice research, diversity analysis, mutation and isogenic line development and linkage analysis, have provided a foundation for the rice genome

Fig. 12.4. The distribution of components of the Vigna angularis complex in Japan collected between 1996-1998.20 Wild and weedy relatives of the Vigna angularis complex have not been reported from Hokkaido. Wild population. Weedy population: Complex population composed of different plant types. Triangle represents the present center of diversity of Vigna angularis complex in Japan.

project (Fig. 12.5). These studies have depended on the genetic diversity of conserved rice germplasm.27

In Japan, initial research into rice varietal diversity worldwide was initiated by Kato and coworkers.28 Since then, Japanese researchers have applied a variety of techniques to understand the varietal diversity of rice in greater depth. The use of isozyme analysis confirmed data from morphological and historic data that southern China and northern Southeast Asia is the center of rice diversity. Clinal variation for different esterase isozyme genotypes was found to radiate from this center.29 Application of RFLP analysis to varietal diversity analysis has helped to provide much greater detail of the varietal differentiation in rice. Kawase et al30 found three distinct clusters of japonica varieties based on RFLP analysis, and these corresponded to varieties from Japan, Southeast Asia and Nepal.

Development of genetic stocks such as mutants and isolines has provided an early foundation for subsequent linkage analysis. In depth linkage analysis began in the early 1960s when Nagao and Takahashi31 first proposed twelve linkage groups corresponding to the haploid chromosome number in rice. Now all of the twelve linkage groups are known and have been associated with respective chromosomes using reciprocal translocation and primary trisomics.32,33

The development of aneuploids in rice and advances in linkage analysis (see reviews by Iwata,34 Kinoshita,35 Khush and Kinoshita36) provided the basis to which molecular marker maps—an early product of the rice genome projects—could be integrated.37,38 Now the rice genome project has entered a new phase, with a wide variety of important genes now being rapidly and accurately located on the rice genome (for reviews of this area see Sasaki and Moore39).

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