Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population

Han, Zhongmin; Hu, Gang; Liu, Hua; Liang, Famao; Lin, Yi Pu; Zhao, Hu; Zhang, Qinghua; Li, Zhixin; Zhang, Qifa; Xing, Yongzhong

doi:10.1007/s00122-019-03440-y

Cited by 22 publications

(19 citation statements)

References 56 publications

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“…However, it often takes long period for back-cross to get near isogenic lines (NIL) lines. Bin map is an alternative strategy to fine-mapping the yield-associated loci applied in sorghum [ 35 ], rice [ 36 ], and maize [ 2 , 13 , 14 , 18 ]. In this study, four husk related QTLs were narrowed from the original 5.1 Mb - 8.9 Mb interval to 0.54 Mb - 2.72 Mb region according to a bin map.…”

Section: Discussionmentioning

confidence: 99%

Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population

Zhang¹,

Ming

Xia

et al. 2021

BMC Genomics

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Background The maize husk consists of numerous leafy layers and plays vital roles in protecting the ear from pathogen infection and dehydration. Teosinte, the wild ancestor of maize, has about three layers of small husk outer covering the ear. Although several quantitative trait loci (QTL) underlying husk morphology variation have been reported, the genetic basis of husk traits between teosinte and maize remains unclear. Results A linkage population including 191 BC2F8 inbred lines generated from the maize line Mo17 and the teosinte line X26–4 was used to identify QTL associated with three husk traits: i.e., husk length (HL), husk width (HW) and the number of husk layers (HN). The best linear unbiased predictor (BLUP) depicted wide phenotypic variation and high heritability of all three traits. The HL exhibited greater correlation with HW than HN. A total of 4 QTLs were identified including 1, 1, 2, which are associated with HL, HW and HN, respectively. The proportion of phenotypic variation explained by these QTLs was 9.6, 8.9 and 8.1% for HL, HN and HW, respectively. Conclusions The QTLs identified in this study will pave a path to explore candidate genes regulating husk growth and development, and benefit the molecular breeding program based on molecular marker-assisted selection to cultivate maize varieties with an ideal husk morphology.

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Section: Discussionmentioning

confidence: 99%

Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population

Zhang¹,

Ming

Xia

et al. 2021

BMC Genomics

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“…Therefore, the information provided in this study will greatly improve recombination detection, haplotype prediction and causal variant identification in the MAGIC population. In fact, even though hundreds of tomato and wild relatives accessions have been already re-sequenced 7 , 42 – 44 , only the sequencing of the MAGIC founders can efficiently exploit the whole potential of MAGIC populations 45 – 47 .…”

Section: Discussionmentioning

confidence: 99%

Morphoagronomic characterization and whole-genome resequencing of eight highly diverse wild and weedy S. pimpinellifolium and S. lycopersicum var. cerasiforme accessions used for the first interspecific tomato MAGIC population

Gramazio¹,

Pereira-Dias²,

Vilanova³

et al. 2020

Hortic Res

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The wild Solanum pimpinellifolium (SP) and the weedy S. lycopersicum var. cerasiforme (SLC) are largely unexploited genetic reservoirs easily accessible to breeders, as they are fully cross-compatible with cultivated tomato (S. lycopersicum var. lycopersicum). We performed a comprehensive morphological and genomic characterization of four wild SP and four weedy SLC accessions, selected to maximize the range of variation of both taxa. These eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross (MAGIC) population. The morphoagronomic characterization was carried out with 39 descriptors to assess plant, inflorescence, fruit and agronomic traits, revealing the broad range of diversity captured. Part of the morphological variation observed in SP was likely associated to the adaptation of the accessions to different environments, while in the case of SLC to both human activity and adaptation to the environment. Whole-genome resequencing of the eight accessions revealed over 12 million variants, ranging from 1.2 to 1.9 million variants in SLC and from 3.1 to 4.8 million in SP, being 46.3% of them (4,897,803) private variants. The genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of SLC. This was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two taxa. The functional characterization of the variants revealed a significative enrichment of GO terms related to changes in cell walls that would have been negatively selected during domestication and breeding. The comprehensive morphoagronomic and genetic characterization of these accessions will be of great relevance for the genetic analysis of the first interspecific MAGIC population of tomato and provides valuable knowledge and tools to the tomato community for genetic and genomic studies and for breeding purposes.

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“…In a MAGIC rice population of over 1316 RILs, the mapping intervals were~700 Kbp on average (Raghavan et al 2017). However, as discussed above, empirical (Descalsota et al 2018) Bacterial leaf streak and bacterial leaf blight (Bossa-Castro et al 2018) Grain shape Grain quality, cooking and taste attributes (Ponce et al 2018) Yield, plant height, heading date, grain quality and biofortification (Zaw et al 2019) Grain length, grain width, grain thickness, and thousand grain weight (Ponce et al 2020) Heading date (Han et al 2020) Sorghum Plant height (Ongom and Ejeta 2018) Strawberry Fruit quality-related traits (Wada et al 2017) Tomato Fruit weight (Pascual et al 2015) Fruit weight and flowering time plasticity in response to water, salinity and heat stress (Diouf et al 2020) mapping resolution may be determined by the QTL effect size and population size. The wheat MAGIC populations developed at CSIRO (four Australian spring wheat founders, Huang et al 2012) and NIAB (eight UK winter wheat founders, Mackay et al 2014) are examples of MPPs that have been used to map genes controlling important yield related traits.…”

Section: Applications Of Mppsmentioning

confidence: 99%

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Scott¹,

Ladejobi²,

et al. 2020

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Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding. Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a

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Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population

Cited by 22 publications

References 56 publications

Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population

Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population

Morphoagronomic characterization and whole-genome resequencing of eight highly diverse wild and weedy S. pimpinellifolium and S. lycopersicum var. cerasiforme accessions used for the first interspecific tomato MAGIC population

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

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