**4. Genome-wide distribution of genetic diversity assessed with SSR markers**

A subset containing 150 accessions were taken from the whole collection (described below) and were genotyped with 274 genome-wide distributed SSR markers. Gene diversity for the varieties in the subset is 0.544. Among them, *Indica* rice shows a higher gene diversity (0.484) than that of *Japonica* rice (0.454). Similarly, non-waxy rice shows a higher gene diversity (0.540) than that of waxy rice (0.515). However, early-seasonal rice shows a higher gene diversity (0.546) than that of late-seasonal rice (0.510) in our case.

Cultivated rice has been intensively selected during its domestication and breeding. Consequently, the genomic regions controlling traits of economic importance are expected to be shaped by this selection. Therefore, characterizing the genome-wide distribution of genetic diversity of cultivated rice germplasm which has been selected for different traits, such as waxy vs. non waxy might help to identify the genes controlling these traits. To do so, as one example, gene diversity was calculated for the waxy rice as well as non-waxy rice for each marker separately across the genome. Similarly, a measurement for genetic distance, modified Roger's distance (MRD) between waxy and non-waxy rice was calculated on an individual marker basis.

Our results indicated that gene diversity for waxy and non-waxy rice varied across the genome (Fig.3). A different degree of divergence (as measured by MRD) between these two germplasm types was observed across the genome (Fig.4).

the main rice production area in our country traditionally and the quantitative traits were

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

2.00

1.87

1.79

1.94

South China Central China Southwest China Northwest China North China

greatly improved by the farmers and breeders through thousands of years selection.

Central China might contribute to the aim more than other regions.

0.73

0.69 0.67

diversity (0.546) than that of late-seasonal rice (0.510) in our case.

germplasm types was observed across the genome (Fig.4).

0.46

Ordered qualitative traits

0.73

0.47 0.46 0.73

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

**4. Genome-wide distribution of genetic diversity assessed with SSR markers**  A subset containing 150 accessions were taken from the whole collection (described below) and were genotyped with 274 genome-wide distributed SSR markers. Gene diversity for the varieties in the subset is 0.544. Among them, *Indica* rice shows a higher gene diversity (0.484) than that of *Japonica* rice (0.454). Similarly, non-waxy rice shows a higher gene diversity (0.540) than that of waxy rice (0.515). However, early-seasonal rice shows a higher gene

Cultivated rice has been intensively selected during its domestication and breeding. Consequently, the genomic regions controlling traits of economic importance are expected to be shaped by this selection. Therefore, characterizing the genome-wide distribution of genetic diversity of cultivated rice germplasm which has been selected for different traits, such as waxy vs. non waxy might help to identify the genes controlling these traits. To do so, as one example, gene diversity was calculated for the waxy rice as well as non-waxy rice for each marker separately across the genome. Similarly, a measurement for genetic distance, modified Roger's distance (MRD) between waxy and non-waxy rice was calculated

Our results indicated that gene diversity for waxy and non-waxy rice varied across the genome (Fig.3). A different degree of divergence (as measured by MRD) between these two

0.79

Quantitative traits

0.000

cultivated regions

on an individual marker basis.

Unordered qualitative traits

0.47

0.50

0.500

1.000

1.500

2.000

The unequal distribution of genetic diversity across the genome could be explained by the selection history of the different genome regions. Therewith, the genome-wide distribution maps of genetic diversity might be a first step to identify the target genes or regions selected during breeding history. For example, genes related to waxy and non-waxy rice might be present in the most divergent genomic regions between these two germplasm types. Common genes under selection in the breeding program of the both germplasm types (e.g. disease resistant genes) might be present in the genomic regions showing the same level of gene diversity and low MRD.

Fig. 3. Green and red lines indicate gene diversity of non-waxy and waxy rice, respectively. Dashed lines indicate the average gene diversity of the corresponding germplasm type. Vertical lines at each point indicate standard error multiplied by 100 which were calculated by bootstrapping across genotypes. Vertical lines at the x axis indicate genetic map positions of the SSR marker on the chromosome.

Fig. 4. Modified Roger's distance (MRD) between waxy and non-waxy rice across the genome. Dashed lines indicate average MRD across the genome and dotted lines average MRD for each chromosome. Vertical lines at the x axis indicate genetic map positions of the SSR markers on the chromosome.
