Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays)

Abstract

Background: Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested.

Results: Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs).

Conclusions: We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.

Keywords: Bin map; Genotyping by sequencing (GBS); High resolution; Minor effect; Plant architecture; Quantitative trait loci (QTLs).

Fig. 1

The genotype profile. a The graphic genotype of 1021 RILs. Red, Zheng58 genotype; Blue, Chang7–2 genotype.Heterozygouse genotypes were set as missing data and imputed by “argmax” method in R/qtl package. b Recombination ratio (outer, pink), gene density (middle, blue) and SNPs density (inner, green) distribution across the ten chromosomes. c, d The distribution of segregation distortions in chromosome 2 and 9. Segregation distortion was test by Chi-test and –log10 (P_Chi-test) were plotted against its physical position. Candidate genes ms32, rf2 were pointed out. Threshold of no distortion (p < 0.01, after Bonferroni-correction) were showed as red dashed lines

Fig. 2

Five silk color QTLs and three putative candidate genes. The silk color QTLs located on chromosomes 1, 4, 6, 9 and 10 were plotted. The positions of candidate genes P1, pl1 and r1 were indicated by vertical dashed lines

Fig. 3

Fifty-one minor effect QTLs for 6 plant architecture traits. The ten chromosomes were displayed as grey bars according to the physical map, unit: Mb. Segments next to the chromosomes with different colors represented different QTLs for traits listed in the legend; Length of segments represented physical intervals of corresponding QTLs. Candidate genes were pointed out by short red dashed lines; red characters: reported mutants; blue characters: candidate genes inferred from homologues; black characters: genes with known function

Fig. 4

Verification of plant height QTL, qPH1a. Two BC₅F₁ ILs and three BC₆F₁ recombinants were genotyped by four Indels markers: Yellow, heterozygous; Green, Zheng58. The heterozygous segment of each ILs would segregate into two types of genotypes in its Zheng58-crossed progenies: homozygous Zheng58 and heterozygous. A simple t-test was performed to test PH difference between these genotypes. If significant difference (p < 0.05) was observed then qPH1a should be localized in the heterozygous region, else in the homozygous region. Finally, qPH1a was defined downstream of 91.18 Mb in chromosome 1. ^aPhysical position for Indels. Rec. number of recombinants found in these progenies