Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne

Pfender, W. F.; Saha, Malay C.; Johnson, Eric A.; Slabaugh, Mary B.

doi:10.1007/s00122-011-1546-3

Cited by 174 publications

(150 citation statements)

References 51 publications

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“…RAD tags were also used to identify three quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in perennial ryegrass (Lolium perenne L.) from crosses between a susceptible and a resistant plant [100].…”

Section: Aflp (Amplified Fragment Length Polymorphisms)mentioning

confidence: 99%

Increasing Food Production in Africa by Boosting the Productivity of Understudied Crops

Tadele

Assefa

2012

Agronomy

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Abstract:The Green Revolution has enabled Asian countries to boost their crop production enormously. However, Africa has not benefitted from this agricultural revolution since it did not consider local, but important crops grown in the continent. In addition to their versatile adaptation to extreme environmental conditions, African indigenous crops provide income for subsistence farmers and serve as staple food for the vast majority of low-income consumers. These crops, which are composed of cereals, legumes, vegetables and root crops, are commonly known as underutilized or orphan crops. Recently, some of these under-researched crops have received the attention of the national and international research community, and modern improvement techniques including diverse genetic and genomic tools have been applied in order to boost their productivity. The major bottlenecks affecting the productivity of these crops are unimproved genetic traits such as low yield and poor nutritional status and environmental factors such as drought, weeds and pests. Hence, an agricultural revolution is needed to increase food production of these under-researched crops in order to feed the ever-increasing population in Africa. Here, we present both the benefits and drawbacks of major African crops, the efforts being made to improve them, and suggestions for some future directions.

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Section: Aflp (Amplified Fragment Length Polymorphisms)mentioning

confidence: 99%

Increasing Food Production in Africa by Boosting the Productivity of Understudied Crops

Tadele

Assefa

2012

Agronomy

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“…Up to now, all QTL studies on perennial ryegrass only involved biparental populations. Their parents could be chosen with opposite phenotypes for the trait of interest as for crown rust resistance in the F1 populations (Dumsday et al 2003;Muylle et al 2005a, b;Pfender et al 2011), for flowering time with the F1 population studied by Byrne et al (2009), for leaf length (F1 population, Barre et al 2009), for biomass in the F2 population in the study of Anhalt et al (2008) or for sugar content (Jones et al 2002b). The parents could also be chosen for their diverse origin: geographical as in the F1 population studied by Faville et al (2004) or in the F2 population described by Jensen et al (2005a), or genetic as in the population p150/112 coming from the cross between a hybrid F1 and a doubled-haploid plant (Jones et al 2002a).…”

Section: Rust Tolerancementioning

confidence: 99%

Detection of favorable alleles for plant height and crown rust tolerance in three connected populations of perennial ryegrass (Lolium perenne L.)

Pauly¹,

Flajoulot²,

Garon³

et al. 2012

Theor Appl Genet

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Plant height, which is an estimator of vegetative yield, and crown rust tolerance are major criteria for perennial ryegrass breeding. Genetic improvement has been achieved through phenotypic selection but it should be speeded up using marker-assisted selection, especially in this heterozygous species suffering from inbreeding depression. Using connected multiparental populations should increase the diversity studied and could substantially increase the power of quantitative trait loci (QTL) detection. The objective of this study was to detect the best alleles for plant height and rust tolerance among three connected populations derived from elite material by comparing an analysis per parent and a multipopulation connected analysis. For the studied traits, 17 QTL were detected with the analysis per parent while the additive and dominance models of the multipopulation connected analysis made it possible to detect 33 and 21 QTL, respectively. Favorable alleles have been detected in all parents. Only a few dominance effects were detected and they generally had lower values than the additive effects. The additive model of the multipopulation connected analysis was the most powerful as it made it possible to detect most of the QTL identified in the other analyses and 11 additional QTL. Using this model, plant growth QTL and rust tolerance QTL explained up to 19 and 38.6% of phenotypic variance, respectively. This example involving three connected populations is promising for an application on polycross progenies, traditionally used in breeding programs. Indeed, polycross progenies actually are a set of several connected populations.

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“…One of the simplest methods is the separation and purification of restriction fragments within a given size range. For example, restriction site-associated DNA (RAD) sequencing has been used to successfully construct high-density genetic map for Lolium perenne and grape (Pfender et al 2011;Wang et al 2012). Based on the next generation sequencing (NGS) technology, specific-locus amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large scale de novo discovery and genotyping of SNP (Sun et al 2013).…”

Section: Introductionmentioning

confidence: 99%

A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq)

Yan

Zhang

Huang

et al. 2015

Planta

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This genetic map for Agropyron Gaertn. contained 1023 markers on seven linkage groups, with a total of 907.8 cM and an average distance of 1.5 cM between adjacent loci. Many wheat- Agropyron cristatum derivative lines exhibit superior agronomic traits, and part of them are valuable for future wheat breeding. To date, no high-density genetic map for Agropyron Gaertn. has been published. Specific-locus amplified fragment sequencing (SLAF-seq), a recently developed strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms (SNPs), was employed in this study to develop sufficient markers for a segregating Agropyron F1 population derived from an interspecific cross between two cross-pollinated diploid collections A. cristatum (L.) Beauv. 'Z1842' and A. mongolicum Keng 'Z2098'. In total, we obtained raw data consisting of 128,932,358 pair-end reads of ~80 bp long after sequencing. Then 69,325 high-quality SLAFs were detected, of which 26,248 SLAFs were polymorphic and 1752 of the polymorphic markers were used for the genetic map construction. The final map contained 1023 markers on the seven linkage groups (LGs), which spanned a total of 907.8 cM with an average number of 146 markers and 89 loci per LG and an average distance of 1.5 cM between adjacent loci. To our knowledge, this map is the densest genetic linkage map for Agropyron so far. Through BLAT alignment of Agropyron SLAF marker sequences with the draft genome assemblies of wheat and barley, the Agropyron LGs were assigned as LG1-7 according to their corresponding homoeologous chromosomal groups of wheat. Results of this study will not only provide a platform for gene/QTL fine mapping, but also serve as a reference to assist the assembling of the P genome sequence in future.

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Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne

Cited by 174 publications

References 51 publications

Increasing Food Production in Africa by Boosting the Productivity of Understudied Crops

Increasing Food Production in Africa by Boosting the Productivity of Understudied Crops

Detection of favorable alleles for plant height and crown rust tolerance in three connected populations of perennial ryegrass (Lolium perenne L.)

A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq)

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