Identification of QTLs for 14 Agronomically Important Traits inSetaria italicaBased on SNPs Generated from High-Throughput Sequencing

Abstract

Foxtail millet (Setaria italica) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long-and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding.

QTL mapping of yield component traits on bin map generated from resequencing a RIL population of foxtail millet (Setaria italica)

“…Genetic linkage map is the basis for QTL mapping and gene cloning. Its application value depends on the number of markers, the saturation of the map, and the uniformity of the distribution of markers on the map [25]. Therefore, a construction of a high-density linkage map could improve the accuracy of QTL mapping [27].…”

“…It is caused by lethality, partial male or female sterility, gametic selection or zygotic selection and/or pollen spine development [31,33], which become more serious in RIL populations because of genetic drift [31] was associated with both natural and artificial selection for several generations [16,34]. Zhang et al [25] found segregation distortion on Chr6 which was significantly distorted toward Zhanggu which may exist intraspecific hybrid pollen sterility, and they located one gene controlling the high male-sterility QTL combined with previous report [35]. Similarly, Fang et al [16] found two gametocidal genes (Gc) on Chr8 by the distorted loci in two SDRs skewed toward different parents.…”

“…Five hundred and twelve loci associated with 47 agronomic traits were identified through genome wide association studies (GWAS). Ni et al [24] and Zhang et al [25] resequenced a RIL population using single seed descent strategy from a cross between Zhanggu and A2, and developed a high-resolution bin map with high-density SNP markers. A total of 69 QTLs for 21 agronomic traits were identified.…”

“…Compared with the previously reported bin-marker genetic maps, the genetic map spanning 1222.26 cM had higher saturation and more markers. For example, Zhang et al[25] constructed a linkage map consisted of 2022 bin markers harboring 33, 579 SNPs, covering 1934.6 cM of the genome. Wang et al…”

Detection of genomic loci associated with chromosomal recombination using high-density linkage mapping in Setaria

“…The benefits of using Setaria as a model species include its small genome, reproductive convenience, abundant genetic variation, and the availability of multiple reference genomes 23 – 26 . Numerous linkage maps have been constructed for foxtail millet using RFLP 27 , 28 , InDel 24 , SSR 29 – 31 and SNP 23 , 32 markers, and genomic features including segregation distortion (SD) and chromosome translocation have been identified in individual crosses. However, the low density of molecular markers used for linkage analysis in Setaria remains an obstacle for further genetic analysis of this emerging model.…”