Mapping Loci That Control Tuber and Foliar Symptoms Caused by PVY in Autotetraploid Potato (<i>Solanum tuberosum</i>L.)

Silva, Washington da; Ingram, Jason T.; Hackett, Christine A.; Coombs, Joseph; Douches, David S.; Bryan, Glenn J.; Jong, Walter De; Gray, Stewart M.

doi:10.1534/g3.117.300264

Cited by 31 publications

(19 citation statements)

References 44 publications

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“…Furthermore, the map provides a statement about the inheritance pattern involved in the transmission of genes aiding in the task of haplotype inference. Although other genetic maps were reported in blueberry, high-density polyploid maps are still lacking, which have been already reported for other autopolyploid crop species (Da Silva et al, 2017; Ferreira et al, 2019; Schlautman et al, 2018; Deo et al, 2020; Mollinari et al, 2020). Moreover, previous blueberry linkage maps were not assembled considering prior genomic information was based on smaller populations, lower marker density and/or, more importantly, did not consider most of the genetic particularities that are intrinsic to a tetraploid system (Rowland et al, 2014; McCallum et al, 2016; Schlautman et al, 2018).…”

Section: Discussionmentioning

confidence: 96%

“…Software such TetraploidSNPmap (Hackett et al, 2017), an updated version of the TetraploidMap (Hackett et al, 2007), polymapR (Bourke et al, 2018), and mappoly ((Mollinari and Garcia, 2019) overcame those limitations and allowed the construction of high-density linkage maps using SNP data and multi-dose markers. Potato (Da Silva et al, 2017), sweetpotato ( Ipomoea batatas L.) (Mollinari et al, 2020) and forage grasses (Ferreira et al, 2019; Deo et al, 2020) are examples of autopolyploid crops that have benefited from the utilization of such modern methodologies in QTL inference and linkage mapping analyses. However, to the best of our knowledge, no high-density linkage map has been built for autotetraploid blueberries.…”

Section: Introductionmentioning

confidence: 99%

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High-Resolution Linkage Map and QTL Analyses for Machine Harvest Traits in Autotetraploid Blueberry

Cappai

Amadeu

Benevenuto

et al. 2020

Preprint

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2Blueberry (Vacciunium corymbosum and hybrids) is an autotetraploid crop whose commercial 3 relevance has been growing steadily during the last twenty years. However, the ever-increasing 4 cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the 5 fruit. Machine harvestability is, therefore, a key trait for the blueberry industry. Understanding 6 the genetic architecture of traits through quantitative trait locus (QTL) mapping is the first step 7 towards implementation of molecular breeding for faster genetic gains. Despite recent advances 8 in software development for autotetraploid genetic mapping, a high-resolution map is still not 9 available for blueberry. In this study, we crafted a map for autotetraploid low-chill highbush 10 blueberry containing 11,292 SNP markers and a total size of 1,953.97 cM (average density of 11 5.78 markers/cM). This map was subsequently used to perform QTL analyses for traits relevant 12 to machine harvesting: firmness, firmness retention, and fruit detachment force. Significant 13 QTL peaks were identified for all the traits. The QTL intervals were further explored for putative 14 candidate genes. Genes related to cell wall remodeling were highlighted in the firmness and 15 firmness retention intervals. For fruit detachment force, transcription factors involved in fruit 16 abscission were detected. Altogether, our findings provide the basis for future fine-mapping and 17 molecular breeding efforts for machine harvesting in blueberry. 18 Keywords: Vaccinium, southern highbush blueberry, firmness, detachment force, polyploid 19 20chromosomal alterations are not only tolerated by plant genomes, but can also drive evolution, for example, 21 promoting speciation (Adams and Wendel, 2005). Polyploid organisms are classified as either allopolyploids 22 or autopolyploids, depending on the degree of divergence between their subgenomes (Brubaker et al., 1999). 23 Autopolyploids, such as blueberry (Vaccinium corymbosum L.), potato (Solanum tuberosum L.), and alfalfa 24 (Medicago sativa L.), contain multiple copies of the same chromosome set, which can all pair and exchange 25 1 Cappai et al. QTL Map for Blueberry Harvest genetic material during gamete formation. In contrast, allopolyploids, such as wheat (Triticum aestivum 26 L.), coffee (Coffea arabica L.), and strawberry (Fragaria ananassa Duch.) contain two or more divergent 27 genomes, which usually show bivalent pairing and have disomic inheritance, like diploid organisms. 28 While in diploid systems the study of allelic inheritance is relatively simple, polysomic inheritance in 29 autopolyploids increases the number of possible genetic configurations and impacts downstream genetic 30 analyses, including linkage map construction and quantitative trait loci (QTL) mapping (Bever and Felber, 31 1992). 32 QTL mapping is the association study between phenotypic and genetic variants usually performed by 33 tracking recombination events of the possible QTL along chromosomes (Broman and Sen, 2009). In 34 b...

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Section: Discussionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

High-Resolution Linkage Map and QTL Analyses for Machine Harvest Traits in Autotetraploid Blueberry

Cappai

Amadeu

Benevenuto

et al. 2020

Preprint

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“…array (Bali et al 2017, da Silva et al 2017. The present study is the first to detect and map potato QTLs associated with resistance to bacterial wilt by saturated linkage map of genome-wide markers.…”

Section: Introductionmentioning

confidence: 93%

“…DNA concentration was measured by the Nanodrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). One microgram of dried DNA from each sample was sent to GeneSeek (Neogen Corporation, Lincoln, NE, USA) to obtain data from the 12K potato V2 SNP array (Bali et al 2017, da Silva et al 2017. The obtained microarray intensity data were analyzed using GenomeStudio Polyploid Clustering Ver 1.0 (Illumina Inc., San Diego, CA, USA) with default parameters and cluster distance of -0.07.…”

Section: Snp Genotypingmentioning

confidence: 99%

QTL analysis of resistance to bacterial wilt caused by <i>Ralstonia solanacearum</i> in potato

Habe¹,

Miyatake

Nunome

et al. 2019

Breed. Sci.

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Ralstonia solanacearum causes bacterial wilt, a soil-borne disease and one of the most important maladies of potato and other Solanaceae crops. We analyzed the resistance of a potato clone to bacterial wilt by quantitative trait locus (QTL) analysis. A resistant diploid potato clone 10-03-30 was crossed with a susceptible diploid clone F 1-1 to generate a diploid, two-way pseudo-testcross F 1 population comprised of 94 genotypes. Dense linkage maps, containing 4,139 single nucleotide polymorphism markers with an average distance of 0.6 and 0.3 cM between markers, were constructed for both parents. The resistance level was evaluated by in vitro inoculation test with R. solanacearum (phylotype I/biovar 4/race 1). Five QTLs (qBWR-1 to-5) were identified on potato chromosomes 1, 3, 7, 10, and 11, and they explained 9.3-18.4% of the phenotypic variance. The resistant parent had resistant alleles in qBWR-2, qBWR-3, and qBWR-4 and susceptible alleles in qBWR-1 and qBWR-5. Accumulation of the resistant alleles in all five QTLs increased the level of resistance compared with that of the resistant parent. This is the first study to identify novel QTLs for bacterial wilt resistance in potato by using genome-wide markers.

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“…Much research has focused on developing theory and methods for QTL analysis in autotetraploids. Methods have been proposed for genetic linkage analysis and QTL mapping in experimental populations of autopolyploid species (Hackett et al, 2001(Hackett et al, , 2014(Hackett et al, , 2017Cao et al, 2005;Xu et al, 2014), and widely practised in QTL mapping analyses in polyploid species (Massa et al, 2015;Da Silva et al, 2017;Massa et al, 2018;Mengist et al, 2018;Bourke et al, 2019;da Silva Pereira et al, 2019). However, these studies have been based on various assumptions that have substantially avoided some complexities of the analyses, but in doing so have ignored some essential features of autotetrasomic inheritance and practical data analysis.…”

Section: Introductionmentioning

confidence: 99%

A tetrasomic inheritance model and likelihood‐based method for mapping quantitative trait loci in autotetraploid species

et al. 2020

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Dissecting the genetic architecture of quantitative traits in autotetraploid species is a methodologically challenging task, but a pivotally important goal for breeding globally important food crops, including potato and blueberry, and ornamental species such as rose. Mapping quantitative trait loci (QTLs) is now a routine practice in diploid species but is far less advanced in autotetraploids, largely due to a lack of analytical methods that account for the complexities of tetrasomic inheritance. We present a novel likelihood-based method for QTL mapping in outbred segregating populations of autotetraploid species. The method accounts properly for sophisticated features of gene segregation and recombination in an autotetraploid meiosis. It may model and analyse molecular marker data with or without allele dosage information, such as that from microarray or sequencing experiments. The method developed outperforms existing bivalent-based methods, which may fail to model and analyse the full spectrum of experimental data, in the statistical power of QTL detection, and accuracy of QTL location, as demonstrated by an intensive simulation study and analysis of data sets collected from a segregating population of potato (Solanum tuberosum). The study enables QTL mapping analysis to be conducted in autotetraploid species under a rigorous tetrasomic inheritance model.

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Mapping Loci That Control Tuber and Foliar Symptoms Caused by PVY in Autotetraploid Potato (Solanum tuberosumL.)

Cited by 31 publications

References 44 publications

High-Resolution Linkage Map and QTL Analyses for Machine Harvest Traits in Autotetraploid Blueberry

High-Resolution Linkage Map and QTL Analyses for Machine Harvest Traits in Autotetraploid Blueberry

QTL analysis of resistance to bacterial wilt caused by <i>Ralstonia solanacearum</i> in potato

A tetrasomic inheritance model and likelihood‐based method for mapping quantitative trait loci in autotetraploid species

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