Development of robust molecular markers for marker-assisted selection of leaf rust resistance gene Lr23 in common and durum wheat breeding programs

Chhetri, Mumta; Bariana, Harbans; Wong, Debbie; Sohail, Younas; Hayden, Matthew; Bansal, Urmil

doi:10.1007/s11032-017-0628-6

Cited by 45 publications

(26 citation statements)

References 22 publications

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“…While marker-assisted selection (MAS) has proven itself a useful tool in crop improvement programs, the approach is most effective when targeting a small number of genes with large effect, such as leaf rust resistance genes (e.g. Lr23 ) in bread and durum wheat [ 26 ] and Yr15 in durum wheat [ 27 ]. In addition, MAS can only be applied if the target gene or quantitative trait loci (QTL) responsible for the trait of interest is known.…”

Section: Introductionmentioning

confidence: 99%

Speed breeding for multiple quantitative traits in durum wheat

et al. 2018

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BackgroundPlant breeding requires numerous generations to be cycled and evaluated before an improved cultivar is released. This lengthy process is required to introduce and test multiple traits of interest. However, a technology for rapid generation advance named ‘speed breeding’ was successfully deployed in bread wheat (Triticum aestivum L.) to achieve six generations per year while imposing phenotypic selection for foliar disease resistance and grain dormancy. Here, for the first time the deployment of this methodology is presented in durum wheat (Triticum durum Desf.) by integrating selection for key traits, including above and below ground traits on the same set of plants. This involved phenotyping for seminal root angle (RA), seminal root number (RN), tolerance to crown rot (CR), resistance to leaf rust (LR) and plant height (PH). In durum wheat, these traits are desirable in environments where yield is limited by in-season rainfall with the occurrence of CR and epidemics of LR. To evaluate this multi-trait screening approach, we applied selection to a large segregating F2 population (n = 1000) derived from a bi-parental cross (Outrob4/Caparoi). A weighted selection index (SI) was developed and applied. The gain for each trait was determined by evaluating F3 progeny derived from 100 ‘selected’ and 100 ‘unselected’ F2 individuals.ResultsTransgressive segregation was observed for all assayed traits in the Outrob4/Caparoi F2 population. Application of the SI successfully shifted the population mean for four traits, as determined by a significant mean difference between ‘selected’ and ‘unselected’ F3 families for CR tolerance, LR resistance, RA and RN. No significant shift for PH was observed.ConclusionsThe novel multi-trait phenotyping method presents a useful tool for rapid selection of early filial generations or for the characterization of fixed lines out-of-season. Further, it offers efficient use of resources by assaying multiple traits on the same set of plants. Results suggest that when performed in parallel with speed breeding in early generations, selection will enrich recombinant inbred lines with desirable alleles and will reduce the length and number of years required to combine these traits in elite breeding populations and therefore cultivars.Electronic supplementary materialThe online version of this article (10.1186/s13007-018-0302-y) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Speed breeding for multiple quantitative traits in durum wheat

et al. 2018

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“…Given the success in related species such as tomato ( Solanum lycopersicum L.), where crack-resistant material has been developed (Matas et al, 2004 ), it seems likely that similar improvement may be expected for the cape gooseberry. Developing resources and increasing genetic knowledge on fruit quality and yield characteristics in the cape gooseberry will accelerate the time of development of new varieties, facilitating the identity of the cultivar, the evaluation of genetic diversity, the selection of parents, and the confirmation of hybrids with the use of Marker Assisted Selection (MAS) (Chhetri et al, 2017 ; Favoretto et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.)

2018

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Association mapping has been proposed as an efficient approach to assist plant breeding programs to investigate the genetic basis of agronomic traits. In this study, we evaluated 18 traits related to yield, (FWP, NF, FWI, and FWII), fruit size-shape (FP, FA, MW, WMH, MH, HMW, DI, FSI, FSII, OVO, OBO), and fruit quality (FIR, CF, and SST), in a diverse collection of 100 accessions of Physalis peruviana including wild, landraces, and anther culture derived lines. We identified seven accessions with suitable traits: fruit weight per plant (FWP) > 7,000 g/plant and cracked fruits (CF) < 4%, to be used as parents in cape gooseberry breeding program. In addition, the accessions were also characterized using Genotyping By Sequencing (GBS). We discovered 27,982 and 36,142 informative SNP markers based on the alignment against the two cape gooseberry references transcriptomes. Besides, 30,344 SNPs were identified based on alignment to the tomato reference genome. Genetic structure analysis showed that the population could be divided into two or three sub-groups, corresponding to landraces-anther culture and wild accessions for K = 2 and wild, landraces, and anther culture plants for K = 3. Association analysis was carried out using a Mixed Linear Model (MLM) and 34 SNP markers were significantly associated. These results reveal the basis of the genetic control of important agronomic traits and may facilitate marker-based breeding in P. peruviana.

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“…Single nucleotide polymorphism (SNP) markers identified in GWA studies can be used to produce efficient tools for MAS in breeding, such as competitive allele specific PCR (KASP) markers. KASP markers developed from SNP sequences flanking the putative QTL regions allow MAS to efficiently track the inheritance of the desired traits, being them agronomic (Cabral et al, 2014 ) or disease related (Dreisigacker et al, 2015 ; Chhetri et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study of Septoria tritici Blotch Resistance in Ethiopian Durum Wheat Landraces

et al. 2017

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Septoria tritici blotch (STB) is a devastating fungal disease affecting durum and bread wheat cultivation worldwide. The identification, development, and employment of resistant wheat genetic material is the key to overcoming costs and limitations of fungicide treatments. The search for resistance sources in untapped genetic material may speed up the deployment of STB genetic resistance in the field. Ethiopian durum wheat landraces represent a valuable source of such diversity. In this study, 318 Ethiopian durum wheat genotypes, for the most part traditional landraces, were phenotyped for resistance to different aspects of STB infection. Phenology, yield and yield component traits were concurrently measured the collection. Here we describe the distribution of STB resistance traits in modern varieties and in landraces, and the relation existing between STB resistance and other agronomic traits. STB resistance sources were found in landraces as well as in modern varieties tested, suggesting the presence of alleles of breeding relevance. The genetic material was genotyped with more than 16 thousand genome-wide polymorphic markers to describe the linkage disequilibrium and genetic structure existing within the panel of genotypes, and a genome-wide association (GWA) study was run to allow the identification of genomic loci involved in STB resistance. High diversity and low genetic structure in the panel allowed high efficiency GWA. The GWA scan detected five major putative QTL for STB resistance, only partially overlapping those already reported in the wheat literature. We report four putative loci for Septoria resistance with no match in previous literature: two highly significant ones on Chr 3A and 5A, and two suggestive ones on Chr 4B and 5B. Markers underlying these QTL explained as much as 10% of the phenotypic variance for disease resistance. We found three cases in which putative QTL for agronomic traits overlapped marker trait association deriving from STB GWA. Our results show that the Ethiopian untapped allelic diversity bears a great value in studying the molecular basis of STB resistance and in breeding for resistance in local and international material.

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Development of robust molecular markers for marker-assisted selection of leaf rust resistance gene Lr23 in common and durum wheat breeding programs

Cited by 45 publications

References 22 publications

Speed breeding for multiple quantitative traits in durum wheat

Speed breeding for multiple quantitative traits in durum wheat

Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.)

Genome-Wide Association Study of Septoria tritici Blotch Resistance in Ethiopian Durum Wheat Landraces

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