**Assessment and Utilization of the Genetic Diversity in Rice (***Orysa sativa* **L.)**

Jin Quan Li and Peng Zhang

*State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University China* 

#### **1. Introduction**

86 Genetic Diversity in Plants

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> The basis for raising crop production and improving crop quality is to breed new varieties. The key to breed new varieties are largely depended on the breakthrough of mining the crop germplasm resources. Therefore, the research and utilization of crop genetic diversity plays an important role on crop improvement in the future. Previous researches have indicated that genetic bottleneck effects existed in the procedure of crop domestication and modern breeding, i.e. the allele variation within wild species and landrace would be lost and result in the reduction of gene diversity during domestication and breeding (Tanksly et al., 1997). The narrow genetic basis would lead to cultivars without resistance to new pets and virus and tolerance to bad environment as well as producing the platform effect of yield. These lost alleles in modern cultivars could only trace back to their original landrace and wild species and be recovered. The original landrace are close to cultivars and possess high genetic diversity and many exotic genes, therewith provide useful germplasm resources for crop breeding.

> Identification, uses and conservation for the genetic diversity within crop germplasm resources are of importance for their sustainable use in plant breeding. The current rapidly development of bioinformatics, genomics, and molecular biology as well as conventional breeding methods provides useful means to mine the desirable genes in the resources.

> Rice (*Oryza sativa* L.) feeds more than 50% of the world's population and is one of the most important crops in the world. Rice genetic resource is the primary material for rice breeding and makes a concrete contribution to global wealth creation and food security. Therefore, understanding its valuable genetic diversity and using it in rice genetic improvement is of importance for raising rice yield and the resistance to biotic and abiotic stress as well as improving rice quality to secure global food supplies. Furthermore, as a model plant of cereal family, two rice genome sequence map have been generated (Goff et al., 2002; Yu et al., 2002) and great progress has been made in gene mining with omics technology. Such researches helps to make use of rice genetic resources however in turn requires to make further insights of rice genetic diversity.

> China is well known as an origin center of cultivated rice, with abundant rice genetic resources. As early as 1920-1964, Ying Ting, An academician of Chinese academy of science, collected more than 7128 rice landrace from all over China as well as some main rice

cultivated countries. As far as we know, the collection is one of the earliest collections for rice germplasm resources and therefore we named it as Ting's collection (Lu et al., 2006). Therefore, this chapter aims to explore effective methods on mining the exotic genes within these novel rice germplasm resources.

### **2. Ting's rice germplasm collection**

The Ting's rice germplasm collection consists of 7128 accessions, which was collected and conserved by Academician and Professor Ying Ting during 1920-1964 from 20 different provinces of China as well as from North Korea, Japan, Philippines, Brazil, Celebes, Java, Oceania, and Vietnam (Fig. 1). Most of them are rice landraces and possess high genetic diversity. Due to that it is one of the earliest systematically rice collections in China and covered most of the Chinese rice cultivated regions, it could serve as an representative for the genetic diversity of Chinese rice germplasm resources.

Most accessions were characterized for taxonomical, geographical, morphological and agronomical descriptors, recorded by the previous laboratory of rice ecology of Chinese academy of agricultural sciences, South China Agricultural College and Guangdong academy of agricultural sciences, China (1961-1965). These recorded traits include 20 unordered qualitative traits, i.e. origin of variety, *indica* vs. *japonica*, paddy vs. upland, waxy vs. non-waxy, grain shape, rice color, grain quality, leaf color, leaf margin color, leaf cushion color, auricle color, inner sheath color, outer sheath color, stem color, leaf-green color, stigma color, glume-tip color, sterile lemma color and glume color; 14 ordered qualitative traits, i.e. early- or late-season, type of maturity, shattering habit, awn, awn length, leaf face pubescence, leaf base pubescence, flag-leaf angle, erect vs. bending leaf, compact vs. loose stem, panicle shape, compact vs. loose rachis-braches, sparse vs. dense glume hair, compact vs. loose glume hair; and 15 quantitative traits, i.e. culm length, culm size, thickness of culm wall, the second internode length, number of panicles per plant, panicle length, panicle size, number of seeds per panicle, grain length, grain length/width ratio, grain size, flag leaf length, flag leaf width, length of elongated uppermost internode, grouth duration. These data provide a good basis for studying their phenotypic genetic diversity as well as core collection construction based on the phenotypes.

#### **3. Genetic diversity of phenotypes of Chinese rice germplasm resources**

About 6500 accessions of rice germplasm resources from the Ting's collection with well passport data were selected and studied for their genetic diversity of phenotypes. The origin, type and distribution of these accessions are listed in Table 1. All the studied rice accessions were classified as five regions, i.e. South China, Central China, Southwest China, Northwest China, and North China.

The genetic diversity index (*I*) was calculated by: *ij ij i j P LogP I N* − = , where *Pij* are the frequency of jth phenotypes for ith traits, and N is the total number of traits.

The average genetic diversity index for the five rice cultivated regions from minimum to maximum are: Southwest China > Central China > Northwest China > South China > North

cultivated countries. As far as we know, the collection is one of the earliest collections for rice germplasm resources and therefore we named it as Ting's collection (Lu et al., 2006). Therefore, this chapter aims to explore effective methods on mining the exotic genes within

The Ting's rice germplasm collection consists of 7128 accessions, which was collected and conserved by Academician and Professor Ying Ting during 1920-1964 from 20 different provinces of China as well as from North Korea, Japan, Philippines, Brazil, Celebes, Java, Oceania, and Vietnam (Fig. 1). Most of them are rice landraces and possess high genetic diversity. Due to that it is one of the earliest systematically rice collections in China and covered most of the Chinese rice cultivated regions, it could serve as an representative for

Most accessions were characterized for taxonomical, geographical, morphological and agronomical descriptors, recorded by the previous laboratory of rice ecology of Chinese academy of agricultural sciences, South China Agricultural College and Guangdong academy of agricultural sciences, China (1961-1965). These recorded traits include 20 unordered qualitative traits, i.e. origin of variety, *indica* vs. *japonica*, paddy vs. upland, waxy vs. non-waxy, grain shape, rice color, grain quality, leaf color, leaf margin color, leaf cushion color, auricle color, inner sheath color, outer sheath color, stem color, leaf-green color, stigma color, glume-tip color, sterile lemma color and glume color; 14 ordered qualitative traits, i.e. early- or late-season, type of maturity, shattering habit, awn, awn length, leaf face pubescence, leaf base pubescence, flag-leaf angle, erect vs. bending leaf, compact vs. loose stem, panicle shape, compact vs. loose rachis-braches, sparse vs. dense glume hair, compact vs. loose glume hair; and 15 quantitative traits, i.e. culm length, culm size, thickness of culm wall, the second internode length, number of panicles per plant, panicle length, panicle size, number of seeds per panicle, grain length, grain length/width ratio, grain size, flag leaf length, flag leaf width, length of elongated uppermost internode, grouth duration. These data provide a good basis for studying their phenotypic genetic diversity as well as core

**3. Genetic diversity of phenotypes of Chinese rice germplasm resources** 

frequency of jth phenotypes for ith traits, and N is the total number of traits.

About 6500 accessions of rice germplasm resources from the Ting's collection with well passport data were selected and studied for their genetic diversity of phenotypes. The origin, type and distribution of these accessions are listed in Table 1. All the studied rice accessions were classified as five regions, i.e. South China, Central China, Southwest China,

The average genetic diversity index for the five rice cultivated regions from minimum to maximum are: Southwest China > Central China > Northwest China > South China > North

*ij ij*

, where *Pij* are the

*P LogP*

*i j*

− =

*N*

*I*

these novel rice germplasm resources.

**2. Ting's rice germplasm collection** 

the genetic diversity of Chinese rice germplasm resources.

collection construction based on the phenotypes.

The genetic diversity index (*I*) was calculated by:

Northwest China, and North China.

China for Unordered qualitative traits, North China > Northwest China > South China > Central China > Southwest China for ordered qualitative traits, and South China > North China > Central China > Northwest China > Southwest China for quantitative traits (Fig.2).

Fig. 1. Rice germplasm resources in Ting's collection and their regeneration. Upper left, preparing seeds for sowing; upper middle, sowing in the nursery field; upper right, transplanted in the field; bottom left, measuring the traits and harvest; bottom middle, a global view for the germplasm regenerating field and their genetic diversity; bottom right, seed cool room with air condition, where the rice seeds are conserved in the block jars.


Table 1. The origin, type and distribution of rice germplasm resources

The results show that the most abundant genetic diversity for rice qualitative traits among the five rice cultivated regions are Southwest China, which is relevant to the geographic location and climate in Yunnan province and Guizhou province of China. The reasons for it might be the high variation in different sea levels (76~2700m) which results in several different climate zone. However, for the genetic diversity in quantitative traits, South and Central China are the highest ones. The reason might be that South and central China are the main rice production area in our country traditionally and the quantitative traits were greatly improved by the farmers and breeders through thousands of years selection.

The results indicated that the rice germplasm resources from Southwest China might help to raise the rice genetic diversity for qualitative traits, such as grain colors, grain quality, etc. For the improvement of quantitative trains, the rice germplasm resources from South and Central China might contribute to the aim more than other regions.

Fig. 2. The average genetic diversity index for rice germplasm resources from different cultivated regions
