Browsing by Subject "Candidate genes"

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Joint QTL analysis of three connected F2-crosses in pigs
(2012) Rückert, Christine; Bennewitz, Jörn
Mapping Quantitative Trait Loci (QTL) has received considerable attention in livestock genetic research over the last two decades. Knowledge of the location, the mode of inheritance and the size of effects of QTL contribute to a deeper understanding of the genetic architecture of quantitative or complex traits. Furthermore, mapped QTL were envisaged for use in so-called marker assisted selection programs. Before the era of genomics started, microsatellites were usually used as genetic markers for QTL mapping. In pigs, F2-crosses were frequently established from divergently selected founder breeds. Usually, the sizes of these F2-experiments are in the range of 300 individuals, which is too small to obtain sufficient statistical power to map QTL precisely. One large F2-experiment was set up in the 90th of the last century at the University of Hohenheim. Three F2-crosses from three genetically different founder breeds (Meishan, Pietrain and European Wild Boar) with almost 1000 individuals were genotyped and phenotyped for around 50 quantitative traits. In further studies, each of the crosses were analysed separately and more complex modes of inheritance were ignored. However, several researchers showed that a combined analysis with several QTL experiments can boost statistical power. Additionally, the mode of inheritance is sometimes not restricted to additive and dominant gene action. The overall aim of this thesis was the joint analysis of these three F2-crosses with more appropriate statistical models and to draw more precise conclusions about the QTL segregating within these experimental designs.
Meta-quantitative trait loci analysis and candidate gene mining for drought tolerance-associated traits in maize (Zea mays L.)
(2024) Li, Ronglan; Wang, Yueli; Li, Dongdong; Guo, Yuhang; Zhou, Zhipeng; Zhang, Mi; Zhang, Yufeng; Würschum, Tobias; Liu, Wenxin
Drought is one of the major abiotic stresses with a severe negative impact on maize production globally. Understanding the genetic architecture of drought tolerance in maize is a crucial step towards the breeding of drought-tolerant varieties and a targeted exploitation of genetic resources. In this study, 511 quantitative trait loci (QTL) related to grain yield components, flowering time, and plant morphology under drought conditions, as well as drought tolerance index were collected from 27 published studies and then projected on the IBM2 2008 Neighbors reference map for meta-analysis. In total, 83 meta-QTL (MQTL) associated with drought tolerance in maize were identified, of which 20 were determined as core MQTL. The average confidence interval of MQTL was strongly reduced compared to that of the previously published QTL. Nearly half of the MQTL were confirmed by co-localized marker-trait associations from genome-wide association studies. Based on the alignment of rice proteins related to drought tolerance, 63 orthologous genes were identified near the maize MQTL. Furthermore, 583 candidate genes were identified within the 20 core MQTL regions and maize–rice homologous genes. Based on KEGG analysis of candidate genes, plant hormone signaling pathways were found to be significantly enriched. The signaling pathways can have direct or indirect effects on drought tolerance and also interact with other pathways. In conclusion, this study provides novel insights into the genetic and molecular mechanisms of drought tolerance in maize towards a more targeted improvement of this important trait in breeding.