Multi-parent advanced generation inter-cross in barley: high-resolution quantitative trait locus mapping for flowering time as a proof of concept

Sannemann, Wiebke; Huang, Bevan Emma; Mathew, Boby; Léon, Jens

doi:10.1007/s11032-015-0284-7

Cited by 115 publications

(100 citation statements)

References 47 publications

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“…An insignificant association of embryo production with plant regeneration, invaluable for the creation of mapping populations for genetic and genomic studies (Forster et al 2007) and the simplification of genome sequence assembly (Dunwell 2010). Through self-pollination, DH populations can be propagated indefinitely and stored as seed, thus allowing for multi-year and multi-location phenotyping for QTL discovery (Guo et al 2013), which has been particularly useful in cereal species (Cabral et al 2014;Sannemann et al 2015;Obsa et al 2016). In breeding programs, DH production replaces inbred line development through repeated self-pollination, so that major reductions in the time to cultivar release are achieved (Dwivedi et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Inheritance patterns of the response to in vitro doubled haploid induction in perennial ryegrass (Lolium perenne L.)

Begheyn

Roulund

Vangsgaard

et al. 2017

Plant Cell Tiss Organ Cult

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Section: Introductionmentioning

confidence: 99%

Inheritance patterns of the response to in vitro doubled haploid induction in perennial ryegrass (Lolium perenne L.)

Begheyn

Roulund

Vangsgaard

et al. 2017

Plant Cell Tiss Organ Cult

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“…Two main types of populations were proposed, Nested Association Mapping, mainly used in maize [11] and Multi-allelic Genetic Intercross (MAGIC), which have been developed in Arabidopsis [12], rice [13], wheat [14], barley [15] and tomato [16]. Multi-parental populations constitute a unique resource that can overcome the main limitations of GWAs and RIL studies and provide complementary information [17].…”

Section: Introductionmentioning

confidence: 99%

Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels

et al. 2016

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Quantitative trait loci (QTL) have been identified using traditional linkage mapping and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of the genetic background on QTL effect has been underlined. Genome-wide association studies (GWAs) were proposed to circumvent these limitations. In tomato, we have shown that GWAs is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure. Nevertheless, GWAs success might be limited due to the low decay of linkage disequilibrium, which varies along the genome in this species. Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage and GWAs by increasing the precision of QTL mapping. We have developed a MAGIC population by crossing eight tomato lines whose genomes were resequenced. We showed the potential of the MAGIC population when coupled with whole genome sequencing to detect candidate single nucleotide polymorphisms (SNPs) underlying the QTLs. QTLs for fruit quality traits were mapped and related to the variations detected at the genome sequence and expression levels. The advantages and limitations of the three types of population, in the context of the available genome sequence and resequencing facilities, are discussed.

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“…Population design varies based on considerations such as mating system and resource availability. Multiparent intercross populations that use more complex crossing designs have been developed in mouse (Churchill et al 2004), Drosophila (Macdonald and Long 2007), Arabidopsis (Kover et al 2009;Huang et al 2011), rice (Bandillo et al 2013), wheat (Rebetzke et al 2014), and barley (Sannemann et al 2015); and backcross-NAM designs have been developed in sorghum (Jordan et al 2011) and barley (Schnaithmann et al 2014;Maurer et al 2015). Notably, with its wide variation in flowering time and disease response, the BC 1 -derived Halle exotic barley (HEB) population has been used to characterize the genetic architecture of flowering time (Maurer et al 2015) and to map seedling leaf-rust resistance (Schnaithmann et al 2014).…”

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Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

et al. 2016

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The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC 2 F 4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r 2 = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for highresolution gene mapping and discovery of novel allelic variation using wild barley germplasm.KEYWORDS wild barley; advanced backcross; nested association mapping population; association mapping; plant genetic resources; Multiparent Advanced Generation Inter-Cross (MAGIC); multiparental populations; MPP D IVERSE germplasm collections are valuable resources for crop improvement. However, breeders often neglect these resources due to the time and effort required to identify and deploy beneficial exotic alleles. Breeding for complex traits requires balancing the introduction of genetic diversity with maintaining the selective progress obtained over many cycles of breeding (Bernardo 2002). Due to the malting quality requirements imposed by North American malting and brewing industries, barley (Hordeum vulgare subsp. vulgare) breeding has been restricted to a narrow germplasm base and focused on elite-by-elite crosses (Rasmusson and Phillips 1997). Over many cycles of breeding, extensive genome-wide linkage disequilibrium (LD) can develop in closed breeding populations (Fang et al. 2013), and the genetic diversity of these populations becomes reduced (Condón et al. 2008;Fu and Somers 2009;Muñoz-Amatriaín et al. 2010;Poets et al. 2015). The need to expand the genetic diversity of the breeding pool has become evident as breeders face disease and environmental pressures which are threatening crop production. Today, genomics technologies are advancing our ability to understand the genetic basis of ...

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Multi-parent advanced generation inter-cross in barley: high-resolution quantitative trait locus mapping for flowering time as a proof of concept

Cited by 115 publications

References 47 publications

Inheritance patterns of the response to in vitro doubled haploid induction in perennial ryegrass (Lolium perenne L.)

Inheritance patterns of the response to in vitro doubled haploid induction in perennial ryegrass (Lolium perenne L.)

Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels

Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

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