Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers

Abstract

Maize is an important cereal crop in the world for feed, food, fodder, and raw materials of industries. Turcicum leaf blight (TLB) is a major foliar disease that can cause more than 50% yield losses in maize. Considering this, the molecular diversity, population structure, and genome-wide association study (GWAS) for TLB resistance were studied in 288 diverse inbred lines genotyped using 89 polymorphic simple sequence repeats (SSR) markers. These lines werescreened for TLB disease at two hot-spot locations under artificially inoculated conditions. The average percent disease incidence (PDI) calculated for each genotype ranged from 17 (UMI 1201) to 78% (IML 12-22) with an overall mean of 40%. The numbers of alleles detected at a locus ranged from twoto nine,with a total of 388 alleles. The polymorphic information content (PIC) of each marker ranged between 0.04 and 0.86. Out of 89 markers, 47 markers were highly polymorphic (PIC ≥ 0.60). This indicated that the SSR markers used were very informative and suitable for genetic diversity, population structure, and marker-trait association studies.The overall observed homozygosity for highly polymorphic markers was 0.98, which indicated that lines used were genetically pure. Neighbor-joining clustering, factorial analysis, and population structure studies clustered the 288 lines into 3–5 groups. The patterns of grouping were in agreement with the origin and pedigree records of the genotypesto a greater extent.A total of 94.10% lines were successfully assigned to one or another group at a membership probability of ≥0.60. An analysis of molecular variance (AMOVA) revealed highly significant differences among populations and within individuals. Linkage disequilibrium for r2 and D′ between loci ranged from 0 to 0.77 and 0 to 1, respectively. A marker trait association analysis carried out using a general linear model (GLM) and mixed linear model (MLM), identified 15 SSRs markers significantly associated with TLB resistance.These 15 markers were located on almost all chromosomes (Chr) except 7, 8, and 9. The phenotypic variation explained by these loci ranged from 6% (umc1367) to 26% (nc130, phi085). Maximum 7 associated markers were located together on Chr 2 and 5. The selected regions identified on Chr 2 and 5 corroborated the previous studies carried out in the Indian maize germplasm. Further, 11 candidate genes were identified to be associated with significant markers. The identified sources for TLB resistance and associated markers may be utilized in molecular breeding for the development of suitable genotypes.

Genetic Variation, DIMBOA Accumulation, and Candidate Gene Identification in Maize Multiple Insect-Resistance

“…When assessing the genetic diversity in maize genotypes, SSR remains the preferred choice due to their co-dominant and multi-allelic nature, abundance, and loci specificity [23]. In the current study, 748 alleles with a range of 2 to 8 per locus were identified among 310 maize inbred lines using 186 polymorphic SSRs (Table S1).…”

“…When various groups (K value) ranging from 1 to 12 were compared, the ∆K reached the maximum value when K = 5, thus the 310 maize inbred lines were divided into five optimal groups (Figure 2A). The inbred lines with a membership probability of ≥0.500 were assigned to the same groups, and if the inbred lines had a membership probability of less than this value, they were assigned to a mixed group (not assigned to any of the five groups) [22,23]. Of the 310 inbred lines, 294 (accounting for 94.84%) were assigned to either one of the five groups, including the Lüda red cob (LRC; 44 lines) group, Tang si ping tou (TSPT; 81 lines) group, Lancaster (Lan; 52 lines) group, P (47 lines) group,…”

Germplasm evaluation and identification of the population source of hard clam (Mercenaria mercenaria) in China using SSR and COI markers

“…Genetic diversity and genetic structure play pivotal roles in population genetic analyses (Ellis and Burke, 2007) and are essential components when assessing germplasm resources of various species. These aspects are crucial for evaluating genetic variation across populations and tracing the origins of species (Tsutsui et al, 2001;Geleta et al, 2006;Kolbe et al, 2007;Merceron et al, 2017;Islam et al, 2018;Slim et al, 2019;Zombardo et al, 2021;Kumar et al, 2022;Khan et al, 2023). Researchers leverage these insights to develop comprehensive conservation strategies tailored to safeguard and explore high-quality germplasm resources (Crozier, 2000;Pertoldi et al, 2007).…”

Marker–Trait Association for Protein Content among Maize Wild Accessions and Coix Using SSR Markers

“…For crop breeding and germplasm management, genome-wide single nucleotide polymorphisms that measure relatedness among distinct inbreds are highly useful [21]. However, SSR markers are also useful to identify the population structure and are considered suitable for association mapping since they are co-dominant, locus-specific, polymorphic, multi-allelic and highly repeatable [22,23]. By utilizing modern breeding tools, we can expedite the breeding process by identifying chromosomal locations and finding significant marker-trait associations through association mapping [24].…”