Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China

Abstract

Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, a panel of foxtail millet elite varieties, which were released in the last sixty years in different geographical regions of China, was characterized using microsatellite markers (SSRs). A clear separation of two subpopulations corresponding to the two eco-geographical regions of foxtail millet production in China was identified by the dataset, which also indicated that in more recently released elite varieties, large quantities of accessions have been transferred from spring-sowing to summer-sowing ecotypes, likely as a result of breeding response to planting configurations. An association mapping study was conducted to identify loci controlling traits of major agronomic interest. Furthermore, selective sweeps involved in improvement of foxtail millet were identified as multi-diverse minor effect loci controlling different agronomic traits during the long-term improvement of elite varieties. Our results highlight the effect of transition of planting configuration and breeding preference on genetic evolvement of crop species.

Fig 1. Inferred population structure of improved varieties.

(A)—(C): Summary plot of estimates of Q. (A) Subclusters of group2 accessions; (B) Two groups inferred in this trial; (C) Subclusters of group1 accessions; (D) Differentiation of genotypes from clusters according to the first three principal components derived from 77 SSR markers diversity analysis; (E) Substructure within each main cluster inferred by STRUCTURE; (F) Distribution of the number of varieties allocated as respective designated subclusters within each province in North China.

Fig 2. Transition of genetic structure of foxtail millet elite varieties in China.

(A) Genetic diversification of varieties released in different periods as revealed by principal component analysis; (B) Relative variation of inferred sub-cluster proportions.