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. 2017 May 5;7(5):1587-1594.
doi: 10.1534/g3.117.041517.

Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing

Kai Zhang  1   2 , Guangyu Fan  3   4   5 , Xinxin Zhang  6   2 , Fang Zhao  7   4   5 , Wei Wei  7   4   5 , Guohua Du  6   2 , Xiaolei Feng  7   4   5 , Xiaoming Wang  7   4   5 , Feng Wang  7   4   5 , Guoliang Song  7   4   5 , Hongfeng Zou  6   2 , Xiaolei Zhang  7   4   5 , Shuangdong Li  7   4   5 , Xuemei Ni  6   2 , Gengyun Zhang  1   2 , Zhihai Zhao  3   4   5
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Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing

Kai Zhang et al. G3 (Bethesda). .

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.

Keywords: QTL mapping; SNP map; agronomic traits; foxtail millet; photoperiod.

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Figures

Figure 1
Figure 1
SNP distribution on the nine foxtail millet chromosomes. SNP, single nucleotide polymorphism.
Figure 2
Figure 2
Recombination bin map constructed using high quality SNPs from sequencing genotyping of the RIL population. Whole map of 2024 recombination bins for the 439 RILs. Chromosomes are separated by vertical gray lines. Chr, chromosome; RIL, recombinant inbred line; SNP, single nucleotide polymorphism.
Figure 3
Figure 3
QTL locations in the genetic map for 14 agronomically important traits under long-day and short-day photoperiods. QTL, quantitative trait loci.
See this image and copyright information in PMC

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