Genetic Diversity, Population Structure and Inter-Trait Relationships of Combined Heat and Drought Tolerant Early-Maturing Maize Inbred Lines from West and Central Africa

Abstract

Adequate knowledge and understanding of the genetic diversity and inter-trait relationships among elite maize inbred lines are crucial for determining breeding strategies and predicting hybrid performance. The objectives of this study were to investigate the genetic diversity of 162 early maturing white and yellow tropical maize inbred lines, and to determine the population structure, heterotic groups and inter-trait relationships among the lines. Using 9684 DArT single nucleotide polymorphism (SNP) markers, a gene diversity (GD) of 0.30 was recorded for the inbred lines with polymorphic information content (PIC) ranging from 0.08 to 0.38. The genetic relatedness among the inbred lines evaluated revealed six different groups based on the history of selection, colour of endosperm and pedigree. The genotype-by-trait (GT) biplot analysis identified inbred 1 (TZEI 935) as outstanding in terms of combined heat and drought (HD) tolerance with the base index analysis identifying 15 superior inbreds in the HD environment. A wide range of genetic variability was observed among the inbred lines, indicating that they are an invaluable resource for breeding for HD tolerance in maize breeding programmes, especially in West and Central Africa.

Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm

“…A total of 15 traits (AD, ASI, EARO, EASP, EPP, HUSKC, LD, LF, PLASP, PLTH, RL, SD, SL, TB, and GY) were used with the 7834 SNPs taking into consideration the population structure and relatedness earlier published [ 33 ]. Sixty-six SNPs were significantly associated with the 15 traits at the threshold ≥3.89 ( Figure 2 a–d; Table S4 ).…”

“…The lines were evaluated at the Manga Station of the Savannah Agricultural Research Institute, Ghana (11°00.977 N, 000°15.912 W) and Kadawa, Nigeria (11°450 N, 8°450 E) in 2018 and 2019 under CHD and TD conditions ( Figure 1 ). Detailed descriptions of the panel of inbred lines used, treatments (CHD and TD), and traits measured have been published in our previous study [ 33 ]. Briefly, the maize plants were exposed to DH.…”

“…The total DArT SNP markers for this panel was 9684 as earlier reported in our study [ 33 ]; further filtering was undertaken in pLINK v1.07 with the indep-pairwise 50 10 0.5 command option [ 53 ], leaving 7834 SNPs of higher quality.…”

“…The MLM adopted was proposed by Yu et al [ 55 ] with each molecular marker considered a fixed effect and assessed individually: where Y is the observed vector of means; β is the fixed effect vector (p × 1) other than molecular marker effects and population structure; α is the fixed effect vector of the molecular markers; ν is the fixed effect vector from the population structure; u is the random effect vector from the polygenic background effect; X , W , and z are the incidence matrices from the associated β , α , ν , and u parameters; and ε is the residual effect vector. This model takes into consideration population structure (Q) and relatedness (K), hence, the Q matrix obtained in the population structure analysis was the same as the one reported earlier by Osuman et al [ 33 ] while the K matrix computed in TASSEL was used. Additionally, to reduce false positive associations, the Bonferroni correction −log P (1/m), where m = number of SNPs, was adopted as the threshold, −log P (1/7834) ≈ 3.89 and this was equivalent to p -value = 1.27 × 10 −4 for declaring the significance of marker–trait association (MTA).…”

“…There is more propelling evidence that the combined effect of heat and drought on plant growth and productivity is more severe than the individual effects of these stresses in several crops including maize [ 25 , 27 , 28 , 29 , 30 , 31 ]. Briefly, combined heat and drought is achieved when the field/plants receive adequate water from planting up to 2–3 weeks before anthesis [ 32 , 33 ], while terminal drought occurs when the field/plants receive adequate water every week from planting up to 32 days after planting [ 33 , 34 ]…”