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Favorable haplotypes and associated genes for flowering time and photoperiod sensitivity identified by comparative selective signature analysis and GWAS in temperate and tropical maize

Author: Zhiwei Li
Author: Xiaogang Liu
Author: Xiaojie Xu
Author: Jiacheng Liu
Author: Zhiqin Sang
Author: Kanchao Yu
Author: Yuxin Yang
Author: Wenshuang Dai
Author: Xin Jin
Author: Yunbi Xu
Year: 2020
ISSN: 2095-5421 (Print)
URI: https://hdl.handle.net/10883/20816
Format: PDF
Language: English
Publisher: Institute of Crop Sciences
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose.
Type: Article
Place of Publication: Netherlands
Place of Publication: Elsevier
Pages: 227-242
Issue: 2
Volume: 8
DOI: 10.1016/j.cj.2019.09.012
Description: On the basis of growing environment, maize can largely be classified into temperate and tropical groups, leaving extensive genetic variation and evolutionary signatures in the maize genome. To identify candidate genes governing flowering time and photoperiod sensitivity, selective signature analysis and SNP- and haplotype-based GWAS were performed using 39,350 high-quality SNP markers in temperate and tropical maize groups consisting of 410 inbred lines phenotyped in three representative experiments in different latitudes. Selective signature analysis revealed 106 selective-sweep regions containing 423 candidate genes involved mainly in biological regulation and biosynthesis pathways. Among these genes, 25 overlapped with known genes governing flowering time and photoperiod sensitivity and 37 were also detected by GWAS for days to tassel, anthesis-silk interval, and photoperiod sensitivity measured by days to silking. Only two of the candidate genes governing flowering time overlapped selective signals. Most haplotype alleles within significant haplotype loci showed the same direction of effect on flowering time and photoperiod sensitivity. The inbred lines carrying GATT at HapL499 (haplotype locus 499) on chromosome 1 had relatively short flowering times. Lines carrying CA at HapL4054 on chromosome 10, TA at HapL4055 on chromosome 10, and GTTGT at HapL978 on chromosome 2 were less sensitive to photoperiod than lines carrying other haplotype alleles. Haplotype loci associated with flowering time and photoperiod sensitivity explained respectively 17.5%?18.6% and 11.2%?15.5% of phenotypic variation. Candidate genes and favorable haplotypes identified in this study may support the more efficient utilization of maize germplasm groups.
Agrovoc: MAIZE
Agrovoc: GENOMES
Agrovoc: FLOWERING
Agrovoc: PHOTOPERIODICITY
Notes: The dataset related with this article is only referential
Related Datasets: https://ars.els-cdn.com/content/image/1-s2.0-S2214514119301540-mmc1.docx
Journal: Crop Journal


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  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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