Genetic Diversity Revealed by SSR Markers and Temporal Trends of Major Commercial Inbred Indica Rice Cultivars in South China in 1949–2005

The genetic diversity of 95 major commercial inbred rice cultivars (Oryza sativa L. subsp. indica) released in South China from 1949 to 2005 were evaluated using 300 simple sequence repeat (SSR) markers distributing evenly on the whole rice genome. A total of 236 polymorphic loci were detected with 776 alleles. The number of allele per locus ranged from 2 to 12 with an average of 3.29. Only 2–4 alleles were found at 206 loci, which accounted for 87.3%. The average polymorphism information content (PIC) value of polymorphic loci was 0.42, which varied with chromosomes. Chromosome 10 had the greatest values in allele number per locus and PIC, and chromosome 5 had the lowest values. The allele number per locus showed an increase trend in the cultivars released from the 1950s to the 1970s and declined afterwards. Analysis of molecular variance (AMOVA) disclosed the significant genetic variation (P < 0.001) among cultivars from different decades, although it only explained 3.77% of the total genetic variation. The genetic distance among cultivars was decreased from the 1950s to the 2000s. According to clustering analysis with COMPLETE method, the 95 cultivars were grouped into 5 clusters at genetic similarity coefficient of 0.685, and several core parents were found in the cultivars released in each decade. The results indicate that the genetic diversity of indica rice cultivars in South China is in a low level and even narrowing after the 1970s. Thus, the genetic basis of indica rice cultivars should be broadened through incorporating new variability into existing rice germplasm in breeding programs. 利用均匀分布于水稻基因组的300个SSR标记对95个华南地区不同年代常规籼稻主栽品种进行分析, 研究该地区常规稻品种的遗传多样性及其变化趋势。检测到236个SSR标记有多态性, 共获得776个等位基因, 每个位点等位基因2∼ 12个, 平均3.29个, 共有206个位点的等位基因数介于2∼ 4个, 占全部多态性位点的87.3%。多态性标记位点的PIC值平均为0.42, 变化范围为0.041∼ 0.790。不同染色体的位点多态性差异显著, 其中第10染色体的位点平均等位基因数最多, PIC值最高, 而第5染色体的位点平均等位基因数最少, PIC值最低; 6个年代中, 50∼ 70年代育成品种包含等位基因数呈显著的上升趋势, 70年代达最高值2.83, 随后逐渐下降。分子方差分析(AMOVA)结果显示不同年代间遗传变异仅占总体变异的3.77%, 但仍达极显著水平(P＜0.001)。不同年代育成品种的遗传距离(GD)呈下降趋势。聚类分析结果显示, 在遗传相似系数(GS)为0.685处可将品种区分为5大类, 表明华南地区各时期的常规稻品种遗传改良都是围绕少数骨干亲本进行的。试验结果显示, 华南地区籼稻品种的遗传多样性狭窄且随年代而变化, 70年代以后呈下降趋势, 在今后的育种中应扩大亲本选材范围、拓宽育种亲本的遗传基础以提高育成品种的遗传多样性。