Four Parent Maize (FPM) Population: Effects of Mating Designs on Linkage Disequilibrium and Mapping Quantitative Traits

Abstract

Core Ideas Intermating did not expand phenotypic variation of quantitative traits in FPM populations. Three intermating generations increased genetic resolution 4‐fold, reducing LD 2.5‐fold. Mating designs had little effect on mapping power, population size was more important. Some intermating is needed to minimize admixture LD in multi‐parent crosses. Surprisingly few QTL were detected, given high heritability and large population size. Multiparent advanced generation inter‐cross (MAGIC) populations can provide improved genetic mapping resolution by increasing allelic diversity and effective recombination. The Four Parent Maize (FPM; Zea mays L.) population implemented five different mating designs used in MAGIC and bi‐parental populations to compare empirical effects on genetic resolution and power of quantitative trait locus (QTL) detection; the combined population here comprised of 1149 individuals with 118,509 genetic markers. Measurements were recorded for plant height (PH), ear height (EH), days to anthesis (DTA) and silking (DTS) in seven environments, spanning three years. Linkage disequilibrium (LD) analysis of subpopulations indicated MAGIC population designs should incorporate generations of intermating to overcome initial LD increase caused by population admixture in a non‐intermated four parent population (4way0sib). A 3‐ to 4‐fold increase in genetic resolution (r2<0.8) and a 2.5‐fold decrease in the extent of LD decay (r2<0.2) compared to the biparental populations was found for the four parent cross at the third generation of intermating (4way3sib). Power of QTL detection was affected to a greater extent by sample size rather than by mating designs. The FPM power simulations indicated that MAGIC populations have the ability to meet or exceed the mapping power of nested association panels with fewer individuals and diversity inputs. Using association mapping software we identified 2, 5, 7, and 6 QTL for PH, EH, DTA, and DTS, respectively. The FPM population is a valuable resource for quantifying empirical improvements of parent number, intermating, and the number of progeny for QTL linkage mapping.

Unoccupied aerial system enabled functional modeling of maize (Zea mays L.) height reveals dynamic expression of loci associated to temporal growth

“…This also demonstrated the lack of statistical power in the smaller of the three populations Tx740xNC356 (n=110). It has been empirically shown that population size is the most critical factor in QTL linkage mapping [24].…”

“…The QTL region of chromosome 3 harbors ZmMADS69 (GRMZM2G171650; Chr3: 158979321..159007265), a regulator of flowering time with pleiotropic effects on plant height. ZmMADS69 has higher expression levels in temperate compared to tropical germplasm, leading to significant detection in temperate by tropical crosses [52], such as LH82xLAMA among others [23, 24, 53]. The identified region on chromosome 1 contained the viviparous8 (vp8; GRMZM2G010353; Chr1: 286390345..286398537) locus which exhibits dwarfism due to reduced cell proliferation [54].…”

Linkage disequilibrium and haplotype block patterns in popcorn populations

“…Higher LD and slower LD decay was observed in biparental and multiparental maize populations [9]. The number and length of haplotype blocks is also highly variable [4,7].…”

“…However, for SNPs separated by up to 100 kb the average was 0.2 (0.03, 0.09, and 0.10 for the biparental, synthetic, and breeding populations, respectively). Even higher LD were reported in the maize NAM (nested association mapping) population[30], and in two biparental and four FPM (four parent maize) populations studied by Anderson, Mahan(9). In general, the average r 2 values observed in the popcorn populations are also lower than the values observed in cattle and chicken populations (0.1 to 0.8 for SNPs separated by up to 100 kb)[31][32][33].The density ranged from 27.8 to 112.3 kb in these three studies.…”

Unoccupied aerial system enabled functional modeling of maize height reveals dynamic expression of loci

“…Maize height is important as a physiological and a highly heritable agronomic trait (Peiffer et al., 2014; Wallace et al., 2016; Anderson, Mahan, Murray, & Klein, 2018; Mahan, Murray, & Klein, 2018; Anderson, Murray, Malambo, et al., 2019) commonly collected due to its ease of measurement, agronomic importance, and correlation to hybrid grain yield in some environment and management scenarios (Mallarino, Oyarzabal, & Hinz, 1999; Machado et al., 2002; Katsvairo, Cox, & Van Es, 2003; Yin, McClure, Jaja, Tyler, & Hayes, 2011; Farfan, Murray, Labar, & Pietsch, 2013; Chen, 2016; Anderson, Murray, Malambo, et al., 2019). Manually measured plant height is commonly collected after reproductive maturity as the distance from the ground to the tip of the tassel, flag leaf, or peduncle.…”