Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Apr 18;13(1):6297.
doi: 10.1038/s41598-023-33250-8.

Genomic-regions associated with cold stress tolerance in Asia-adapted tropical maize germplasm

Kumari Shikha  1 , Vinayan Madhumal Thayil  2 , J P Shahi  1 , P H Zaidi  3 , Kaliyamoorthy Seetharam  3 , Sudha K Nair  3 , Raju Singh  4 , Garg Tosh  5 , Ashok Singamsetti  1 , Saurabh Singh  1 , B Sinha  1
Affiliations

Genomic-regions associated with cold stress tolerance in Asia-adapted tropical maize germplasm

Kumari Shikha et al. Sci Rep. .

Abstract

Maize is gaining impetus in non-traditional and non-conventional seasons such as off-season, primarily due to higher demand and economic returns. Maize varieties directed for growing in the winter season of South Asia must have cold resilience as an important trait due to the low prevailing temperatures and frequent cold snaps observed during this season in most parts of the lowland tropics of Asia. The current study involved screening of a panel of advanced tropically adapted maize lines to cold stress during vegetative and flowering stage under field conditions. A suite of significant genomic loci (28) associated with grain yield along and agronomic traits such as flowering (15) and plant height (6) under cold stress environments. The haplotype regression revealed 6 significant haplotype blocks for grain yield under cold stress across the test environments. Haplotype blocks particularly on chromosomes 5 (bin5.07), 6 (bin6.02), and 9 (9.03) co-located to regions/bins that have been identified to contain candidate genes involved in membrane transport system that would provide essential tolerance to the plant. The regions on chromosome 1 (bin1.04), 2 (bin 2.07), 3 (bin 3.05-3.06), 5 (bin5.03), 8 (bin8.05-8.06) also harboured significant SNPs for the other agronomic traits. In addition, the study also looked at the plausibility of identifying tropically adapted maize lines from the working germplasm with cold resilience across growth stages and identified four lines that could be used as breeding starts in the tropical maize breeding pipelines.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Performance of entries across vegetative, flowering and across season datasets.
Figure 2
Figure 2
Scatter plot, frequency distribution and correlations coefficients among the traits recorded across cold stress locations (L2 to L5).
Figure 3
Figure 3
LD-decay (A), scatter plots of 10 PCs (B) and population structure as expressed by first two PCs (C) observed among the panel of Asia-adapted tropical lines.
Figure 4
Figure 4
Manhattan plot representing the regions significantly associated with grain yield under vegetative (veg), flowering (flow) and across (across) location datasets.
See this image and copyright information in PMC

References

    1. FAO Stat. Food and Agricultural Organization of the United Nation. Economic and Social Department. Statistic Division (ESS). Retrieved from FAO STAT website: http://www.fao.org/about/whowe-are/departments/statistics-division/en (2018).
    1. Prasanna BM, Mazumdar S, Chakraborti M, Hossain F, Manjaiah KM, Agrawal PK, Gupta HS. Genetic variability and genotype× environment interactions for kernel iron and zinc concentrations in maize (Zea mays L.) genotypes. Indian J. Agric. Sci. 2011;81:704.
    1. Lee M, Sharopova N, Beavis WD, Grant D, Katt M, Blair D, Hallauer A. Expanding the genetic map of maize with the intermated B73× Mo17 (IBM) population. Plant Mol. Biol. 2002;48:453–461. doi: 10.1023/A:1014893521186. - DOI - PubMed
    1. Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT StringTie and Ballgown. Nat. Protocol. 2016;11:1650–1667. doi: 10.1038/nprot.2016.095. - DOI - PMC - PubMed
    1. Reeves P, Coupland G. Analysis of flowering time control in Arabidopsis by comparison of double and triple mutants. Plant Physiol. 2001;126:1085–1091. doi: 10.1104/pp.126.3.1085. - DOI - PMC - PubMed

Publication types