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. 2022 May;297(3):873-888.
doi: 10.1007/s00438-022-01894-2. Epub 2022 Apr 22.

Genome-wide identification of quantitative trait loci for morpho-agronomic and yield-related traits in foxtail millet (Setaria italica) across multi-environments

Tianpeng Liu  1   2 , Jihong He  2 , Kongjun Dong  2 , Xuewen Wang  3 , Lei Zhang  2 , Ruiyu Ren  2 , Sha Huang  1 , Xiaoting Sun  1 , Wanxiang Pan  4 , Wenwen Wang  1 , Peng Yang  1 , Tianyu Yang  5 , Zhengsheng Zhang  6
Affiliations

Genome-wide identification of quantitative trait loci for morpho-agronomic and yield-related traits in foxtail millet (Setaria italica) across multi-environments

Tianpeng Liu et al. Mol Genet Genomics. 2022 May.

Abstract

Foxtail millet (Setaria italica) is an ideal model of genetic system for functional genomics of the Panicoideae crop. Identification of QTL responsible for morpho-agronomic and yield-related traits facilitates dissection of genetic control and breeding in cereal crops. Here, based on a Yugu1 × Longgu7 RIL population and genome-wide resequencing data, an updated linkage map harboring 2297 bin and 74 SSR markers was constructed, spanning 1315.1 cM with an average distance of 0.56 cM between adjacent markers. A total of 221 QTL for 17 morpho-agronomic and yield-related traits explaining 5.5 ~ 36% of phenotypic variation were identified across multi-environments. Of these, 109 QTL were detected in two to nine environments, including the most stable qLMS6.1 harboring a promising candidate gene Seita.6G250500, of which 70 were repeatedly identified in different trials in the same geographic location, suggesting that foxtail millet has more identical genetic modules under the similar ecological environment. One hundred-thirty QTL with overlapping intervals formed 22 QTL clusters. Furthermore, six superior recombinant inbred lines, RIL35, RIL48, RIL77, RIL80, RIL115 and RIL125 with transgressive inheritance and enrichment of favorable alleles in plant height, tiller, panicle morphology and yield related-traits were screened by hierarchical cluster. These identified QTL, QTL clusters and superior lines lay ground for further gene-trait association studies and breeding practice in foxtail millet.

Keywords: Linkage map; Morpho-agronomic trait; QTL; Setaria italica; Yield-related traits.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Fig. 1
Fig. 1
The correlation analysis based on the average of 17 traits at all test environments
Fig. 2
Fig. 2
SNP/InDels variations distribution and bin map on Yugu1 × Longgu7 RIL population. a SNPs/InDels density map on nine chromosomes; b SNP/InDels variations distributed on the genome-wide; c The map harboring 2099 bin and 74 SSR markers in the RIL population. d The heatmap for genotypic data checking by pairwise recombination fractions (upper left) and logarithm (base 10) of odds (LOD) scores. Red corresponds to complete linkage markers, whereas blue indicates markers with reasonable order and pairwise recombination fractions
Fig. 3
Fig. 3
Genetic map and QTL for 17 morpho-agronomic and yield-related traits in the RIL population. The ruler with number on the left indicates the genetic distance in centimorgans (cM). The color intensity on the map represents the marker density. The colors marked by I, II, III, IV, V, VI, VII, VIII, IX represent the one QTL detected on 1, 2, 3, 4, 5, 6, 7, 8 or 9 environments, respectively
Fig. 4
Fig. 4
The stable QTL identified in two to six combined environments
Fig. 5
Fig. 5
Box plot of over-parent traits of RILs identified by cluster analysis. *, **, *** represent significant differences at P < 0.05, 0.01 and 0.001, respectively. NS indicates no significant difference
See this image and copyright information in PMC

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