At the same time, many traits are directly related to the subsets. The association of single nucleotide polymorphisms in chicken Lmbr1 intron with chicken polydactyl. Genet. The gene SALL4 encodes a putative zinc finger transcription factor and plays a role in modulating embryonic stem cell pluripotency and early embryonic development (Zhang et al. Copyright © 2020 by the Genetics Society of America, Allen, J., D. Scott, M. Illingworth, B. Dobrzelecki, D. Virdee. QTNs located in at least two environments or detected using two different methods were considered to be significant. 5% and 1% genome-wide significance levels were calculated following the Bonferroni correction: Where Ga is the length genetic map of each chromosome and Gc is the length of the genetic map of all autosomal chromosomes.
Chem. The most significant SNP, GGaluGA132178, was located on GGA2 at 6641.2 kb (P = 7.94 × 10-7), 9.5 kb downstream of dipeptidyl-peptidase 6, transcript variant 3 (DPP6). Zhang et al. Genes highly expressed in stems according to the Phytozome website (https://phytozome.jgi.doe.gov) were searched for in the interval of LD decay distance when r2 dropped to 0.2 on both sides of the QTN. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). Haploview: analysis and visualization of LD and haplotype maps. We do not retain these email addresses. Family-based designs for genome-wide association studies. The editor and reviewers' affiliations are the latest provided on their Loop research profiles and may not reflect their situation at the time of review. Song et al. The kinship matrix used in the analysis process was also calculated by the software. There are two parents, Dongnong L13 (110 cm) and Heongong 60 (70 cm), with significant differences in plant height, were distributed among 156 families. Glyma.04G030400 is involved in all carbohydrate pathways in the cell. Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. 36 (4), 877–882. doi: 10.1007/s12686-011-9548-7, Fang, C., Ma, Y., Wu, S., Liu, Z., Wang, Z., Yang, R., et al. 2010). 2013), egg production and quality (Liu et al. The additive effects of qPH-F-1 detected in the E8 environment were negative, indicating that the allele derived from the male parent “Henong 60” increased plant height. Acta Agronomica Sin. QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. The polarity protein Par6 induces cell proliferation and is overexpressed in breast cancer. 2011).

2010). A total of 10,000 permutations were computed to determine 5% and 1% chromosome-wide significance levels. Analysis and answers to frequently asked questions in quantitative trait locus mapping. One (I) to five (M) QTLs mapped to each linkage group with LOD values between 2.54 and 13.46, and each QTL explained between 0.55% and 19.55% of the phenotypic variation. As shown in Figure 1 and Table 3, four SNPs associated with polydactyly were of genome-wide significance, and three SNPs had suggestive significance. 43, 159–162. Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean (Glycine max) germplasm. Calculating ΔK using STRUCTURE 2.3.4 (Figure 3A, K = 1–10), revealing two subgroups (K = 2) based on the ΔK value (Figure 3B). 33, 408. doi: 10.1038/nbt.3096, Keywords: soybean, plant height, quantitative trait nucleotides, multi-locus genome-wide association studies, linkage analysis, Citation: Fang Y, Liu S, Dong Q, Zhang K, Tian Z, Li X, Li W, Qi Z, Wang Y, Tian X, Song J, Wang J, Yang C, Jiang S, Li W-X and Ning H (2020) Linkage Analysis and Multi-Locus Genome-Wide Association Studies Identify QTNs Controlling Soybean Plant Height.
Conserv. 2010). Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1. Merr.). A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Methodological implementation of mixed linear models in multi-locus genome-wide association studies. LOD values were 2.58 to 13.46, and the PVE ranged from 0.55% to 14.83%. 44, 784–791. Biochemical and functional characterization of inositol 1, 3, 4, 5, 6-pentakisphosphate 2-kinases. U. S. A 108, 6893–6898. doi: 10.13597/j.cnki.maize.science.2013.02.010, Liu, R., Gong, J., Xiao, X., Zhang, Z., Li, J., Liu, A., et al. Here, we carried out phenotypic analysis of 156 recombinant inbred lines derived from “Dongnong L13” and “Henong 60” in nine environments at four locations over 6 years using interval mapping and inclusive composite interval mapping methods. Plant Physiol. SMA is generally used in the case of few molecular markers, and genetic map construction is difficult. The population structure was assessed by multidimensional scaling (MDS) analysis using PLINK software 1.07 (Purcell et al. 11:9. doi: 10.3389/fpls.2020.00009. 10, 826–839.

Crop Sci. 5, e1000551. Genome-wide association study identifies loci and candidate genes for body composition and meat quality traits in Beijing-You chickens. In chickens, GWAS have been performed for growth and meat quality (Gu et al. Polydactyly is a common limb malformation in human, mouse, chicken, and other vertebrates characterized by supernumerary digits. LOD values were between 2.54 and 13.46, and the phenotypic variation explained (PVE) ranged from 1.45% to 19.55%. We identified 21 QTLs in two or more environments, distributed over 14 linkage groups except D1b, A1, C2, B2, E, and I (Table S3). 2008; Grover et al. (2011) consider that linkage analysis and association analysis together are more accurate and effective than single analysis methods in revealing the genetic mechanisms of traits. In addition, for ICIM-ADD, the PIN value was set to 0.001. Plant height is a typical quantitative trait, and also affects soybean yield. In statistics, confounding factors refer to irrelevant variable that are related to both dependent variables and independent variables (Miller, 2005). Two of six BJY males in the F0 generation had polydactyly. Principal components analysis corrects for stratification in genome-wide association studies. We identified 19 homologous genes in Arabidopsis, two of which may regulate plant height and development. Natl. Five genes were in the interval 11.08–12.08 Mb and 25 genes in the interval 42.80–43.00 Mb on chromosome 13, and three genes were in the interval 10.84–11.04 Mb and 29 in the interval 2.36–2.56 Mb on chromosome 4. The range of RIL6013 is large than population conducted by “Minsoy” and “Noir 1”, indicated this population is more suitable for QTL mapping. Genet.

Quantitative trait loci analysis for the developmental behavior of soybean (Glycinemax L. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. 4, 359–361. Plants with marginal utility were avoided during the survey, and 10 plants were randomly selected from each plot to conduct field investigations to determine plant height. The QTL on GGA2 was also found in previous studies in chicken (Dunn et al. 2001; Maas and Fallon 2004; Sagai et al. The recombination rate of the map was 2.9 cM/Mb. doi: 10.2135/cropsci2006.01.0003, Haley, C. S., Knott, S. A. These two subgroups contain 64 (46.04%) and 75 (53.96%) lines, respectively. From a breeding point of view, except in E8, the plant height of the parents fell within the range of [Mean−STD, Mean+STD] for the population, indicating that the population has strong transgressive heterosis and plant height breeding goals will have a larger choice within the population. 2005). Genetics 121, 185–199. Proc. 2008), which was calculated on the basis of the estimated number of independent markers and LD blocks in all chromosomes. Figure 2 Total numbers of QTLs detected across multiple environments and by multiple methods. Yield and yield components of early maturing soybean genotypes in the mid-south. Genetic linkage and genome-wide association studies identify the genetic variation that are contributing to a trait. doi: 10.1007/s11703-007-0001-3, Guzman, P. S., Diers, B. W., Neece, D. J., Martin, S. K. S., Leroy, A. R., Grau, C. R., et al. The GWAS results obtained here were in accord with the linkage analysis on GGA2 and obtained more detail of relevant SNPs. 2010), and eijklmn is the random residual effect.

(2016). No significant QTN was identified in environments E2, E4, or E7. (2015).