The impact of modern plant breeding on dominant Chinese wheat cultivars (Triticum aestivum L.) revealed by SSR and functional markers

The modern plant breeding is generally considered to be a practice that leads to a narrowing in genetic diversity of crops. The objective of the present study was to assess whether this practice has led to the reduction of genetic diversity in modern Chinese wheat cultivars. A set of 80 dominant Chinese wheat cultivars released from 1942 to 2011 was used to describe the genetic diversity based on 137 simple sequence repeat (SSR) and 52 functional markers. Several important properties about the genetic diversity were revealed. First, relative low genetic diversity level was detected on a genome-wide scale. A total of 752 alleles were detected with a range from 1 to 15, and the mean polymorphic information content value was 0.53 with a range from 0.00 to 0.87. Second, the genetic diversity significantly decreased from 2001 to 2011 at the genome-wide level. More importantly, significant differences of genetic diversity among the three different genomes were observed by the analysis of variance (ANOVA). The three genomes had clearly different changing trends over time: the A genome displayed a decreasing trend (regression coefficient (b) = -0.01); in contrast, the other two genomes, B and D, showed the increasing trends (b = 0.01 for the B genome, P = 0.05; b = 0.01 for the D genome, P = 0.05). Third, the analysis of qualitative variations in allelic composition over time indicated that, the more recent the cultivars were, the more similar they were to each other. Finally, the frequencies of favorable alleles related to important agronomic traits had been increasing over time or maintained high frequencies in all seven temporal groups. These findings indicate that modern wheat breeding results in not only a qualitative, but also a quantitative change in genetic diversity in the dominant Chinese wheat cultivars. A special attention should be paid to broaden the genetic base in the A genome.