Identification of bioconversion quantitative trait loci in the interspecific cross Sorghum bicolor × Sorghum propinquum

For lignocellulosic bioenergy to be economically viable, genetic improvements must be made in feedstock quality including both biomass total yield and conversion efficiency. Toward this goal, multiple studies have considered candidate genes and discovered quantitative trait loci (QTL) associated with total biomass accumulation and/or grain production in bioenergy grass species including maize and sorghum. However, very little research has been focused on genes associated with increased biomass conversion efficiency. In this study, Trichoderma viride fungal cellulase hydrolysis activity was measured for lignocellulosic biomass (leaf and stem tissue) obtained from individuals in a F₅ recombinant inbred Sorghum bicolor × Sorghum propinquum mapping population. A total of 49 QTLs (20 leaf, 29 stem) were associated with enzymatic conversion efficiency. Interestingly, six high-density QTL regions were identified in which four or more QTLs overlapped. In addition to enzymatic conversion efficiency QTLs, two QTLs were identified for biomass crystallinity index, a trait which has been shown to be inversely correlated with conversion efficiency in bioenergy grasses. The identification of these QTLs provides an important step toward identifying specific genes relevant to increasing conversion efficiency of bioenergy feedstocks. DNA markers linked to these QTLs could be useful in marker-assisted breeding programs aimed at increasing overall bioenergy yields concomitant with selection of high total biomass genotypes.     

QTL mapping in autotetraploids using SNP dosage information

Key message

Dense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci.

Abstract

Recent developments in sequencing and genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, the SNP genotypes are informative about allele dosage, and Hackett et al. (PLoS ONE 8:e63939, 2013) presented theory about how dosage information can be used in linkage map construction and quantitative trait locus (QTL) mapping for an F₁ population in an autotetraploid species. Here, QTL mapping using dosage information is explored for simulated phenotypic traits of moderate heritability and possibly non-additive effects. Different mapping strategies are compared, looking at additive and more complicated models, and model fitting as a single step or by iteratively re-weighted modelling. We recommend fitting an additive model without iterative re-weighting, and then exploring non-additive models for the genotype means estimated at the most likely position. We apply this strategy to re-analyse traits of high heritability from a potato population of 190 F₁ individuals: flower colour, maturity, height and resistance to late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematode (Globodera pallida), using a map of 3839 SNPs. The approximate confidence intervals for QTL locations have been improved by the detailed linkage map, and more information about the genetic model at each QTL has been revealed. For several of the reported QTLs, candidate SNPs can be identified, and used to propose candidate trait genes. We conclude that the high marker density is informative about the genetic model at loci of large effects, but that larger populations are needed to detect smaller QTLs.     

Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.)

Key message

We have identified QTLs for stomatal characteristics on chromosome II of faba bean by applying SNPs derived from M. truncatula , and have identified candidate genes within these QTLs using synteny between the two species.

Abstract

Faba bean (Vicia faba L.) is a valuable food and feed crop worldwide, but drought often limits its production, and its genome is large and poorly mapped. No information is available on the effects of genomic regions and genes on drought adaptation characters such as stomatal characteristics in this species, but the synteny between the sequenced model legume, Medicago truncatula, and faba bean can be used to identify candidate genes. A mapping population of 211 F₅ recombinant inbred lines (Mélodie/2 × ILB 938/2) were phenotyped to identify quantitative trait loci (QTL) affecting stomatal morphology and function, along with seed weight, under well-watered conditions in a climate-controlled glasshouse in 2013 and 2014. Canopy temperature (CT) was evaluated in 2013 under water-deficit (CTd). In total, 188 polymorphic single nucleotide polymorphisms (SNPs), developed from M. truncatula genome data, were assigned to nine linkage groups that covered ~928 cM of the faba bean genome with an average inter-marker distance of 5.8 cM. 15 putative QTLs were detected, of which eight (affecting stomatal density, length and conductance and CT) co-located on chromosome II, in the vicinity of a possible candidate gene—a receptor-like protein kinase found in the syntenic interval of M. truncatula chromosome IV. A ribose-phosphate pyrophosphokinase from M. truncatula chromosome V, postulated as a possible candidate gene for the QTL for CTd, was found some distance away in the same chromosome. These results demonstrate that genomic information from M. truncatula can successfully be translated to the faba bean genome.     

Identification of quantitative trait loci and candidate genes for specific cellular resistance responses against Didymella pinodes in pea

Key message

Phenotyping of specific cellular resistance responses and improvement of previous genetic map allowed the identification of novel genomic regions controlling cellular mechanisms involved in pea resistance to ascochyta blight and provided candidate genes suitable for MAS.

Abstract

Didymella pinodes, causing ascochyta blight, is a major pathogen of the pea crop and is responsible for serious damage and yield losses. Resistance is inherited polygenically and several quantitative trait loci (QTLs) have been already identified. However, the position of these QTLs should be further refined to identify molecular markers more closely linked to the resistance genes. In previous works, resistance was scored visually estimating the final disease symptoms; in this study, we have conducted a more precise phenotyping of resistance evaluating specific cellular resistance responses at the histological level to perform a more accurate QTL analysis. In addition, P665 × Messire genetic map used to identify the QTLs was improved by adding 117 SNP markers located in genes. This combined approach has allowed the identification, for the first time, of genomic regions controlling cellular mechanisms directly involved in pea resistance to ascochyta blight. Furthermore, the inclusion of the gene-based SNP markers has allowed the identification of candidate genes co-located with QTLs and has provided robust markers for marker-assisted selection.     

Co-suppression of synthesis of major α-kafirin sub-class together with γ-kafirin-1 and γ-kafirin-2 required for substantially improved protein digestibility in transgenic sorghum

Key message

Co-suppressing major kafirin sub-classes is fundamental to improved protein digestibility and nutritional value of sorghum. The improvement is linked to an irregularly invaginated phenotype of protein bodies.

Abstract

The combined suppression of only two genes, γ kafirin-1 (25 kDa) and γ-kafirin-2 (50 kDa), significantly increases sorghum kafirin in vitro digestibility. Co-suppression of a third gene, α-kafirin A1 (25 kDa), in addition to the two genes increases the digestibility further. The high-digestibility trait has previously only been obtained either through the co-suppression of six kafirin genes (α-A1, 25 kDa; α-B1, 19 kDa; α-B2, 22 kDa; γ-kaf1, 27 kDa; γ-kaf 2, 50 kDa; and δ-kaf 2, 18 kDa) or through random chemical-induced mutations (for example, the high protein digestibility mutant). We present further evidence that suppressing just three of these genes alters kafirin protein cross-linking and protein body microstructure to an irregularly invaginated phenotype. The irregular invaginations are consistent with high pepsin enzyme accessibility and hence high digestibility. The approach we adopted towards increasing sorghum protein digestibility appears to be an effective tool in improving the status of sorghum as a principal supplier of energy and protein in poor communities residing in marginal agro-ecological zones of Africa.     

Mapping quantitative trait loci for tissue culture response in VCS3M-DH population of Brassica rapa

Key message

Quantitative trait loci (QTL) controlling callus induction and plant regeneration were identified in the VCS3M-DH population of Brassica rapa.

Abstract

Quantitative trait loci (QTL) controlling callus induction and plant regeneration were identified in the VCS3M-DH population of Brassica rapa. The VCS3M-DH population showed wide and continuous variation in callus induction and shoot regeneration. Significant coefficient correlations were detected between these two parameters. Broad-sense heritability (h ²) for the two traits was around 0.7, indicating genetic regulation of regeneration ability in this population. In the composite interval mapping analysis, two QTLs for callus induction ability, qCi2 and qCi7, were mapped on chromosome A02 and A07, explaining 28.6 % of phenotypic variation. For plant regeneration, four QTLs, qPr6-1 qPr6-2, qPr7, and qPr9 were identified on chromosome A06, A07, and A09, which in total explained 50.1 % of phenotypic variation. Furthermore, 15 putative candidate genes were found on the interval of the six QTLs, which were related to various plant hormones, MADS-box genes, and serine/threonine related genes. These results provide important information to identify genes related to tissue culture ability in B. rapa.     

Water uptake efficiency and above- and belowground biomass development of sweet sorghum and maize under different water regimes

Background and aims

Lately sweet sorghum (S) has attracted great interest as an alternative feedstock for biofuel production due to its high yielding potential and better adaptation to drought than maize (M). However, little is known about the response of newly developed sweet sorghum genotypes to water deficits, especially at the root level and its water uptake patterns. The objective of this study was to compare the water uptake capacity, growth and developmental characteristics at the root and canopy levels of a sweet sorghum hybrid (Sorghum bicolor cv. Sucro 506) with those of maize (Zea mays cv. PR32F73) at two water regimes.

Methods

The trial was setup in a total of 20 rhizotrons (1?m³), where calibrated soil moisture probes were installed for monitoring and adjusting the soil moisture content to 25% (well-watered, W) and 12% (drought stress, D).

Results

DS was able to sustain its physiological activity close to that of WS plants, while maize was not. The biomass production potential of DS was reduced about 38%, while in maize the reduction was 47%. The water use efficiency (WUE), however, was increased by 20% in sweet sorghum and reduced in 5% in maize. Moreover, in contrast to maize the root length density and water uptake capacity of DS was enhanced. Root water uptake efficiency in DM was sustained close to its potential, but not in sweet sorghum.

Conclusions

In summary, the better adaptation to drought of sweet sorghum is explained by increased WUE, sustained physiological activity and enlarged root system. It is also associated with a reduced water uptake efficiency compared to its control but maintained compared to maize.     

Heritability and identification of QTLs and underlying candidate genes associated with the architecture of the grapevine cluster (Vitis vinifera L.)

Key message

We have identified 19 QTLs for rachis architecture, a key and complex trait for grapevine production. Fifty out of 1,173 genes underlying these QTLs are candidates to be further explored.

Abstract

In the table grape industry, the rachis architecture has economic and management implications. Therefore, understanding the genetics of this trait is key for its breeding. The aim of this work was to identify genetic determinants of traits associated with the cluster architecture. Characterisations of eight traits was performed on a ‘Ruby Seedless’ × ‘Sultanina’ crossing (F₁: n = 137) during three seasons, with and without gibberellic acid (GA₃) applications. The genotypic effects and the genotype × GA₃ interactions were significant for several traits. Rachis length (rl), lateral shoulder length and node number along the central axis were the most prominent traits. On average, the heritability of these traits was ~71 %, with heritability of rl being 76 % as estimated under different seasons. Quantitative trait loci (QTLs) analyses showed that linkage group 5 (LG₅) and LG₁₈ harboured the largest number of QTLs for these traits. According to the variance explained, the main QTL (corresponding to rl) was found on LG₉. These QTLs were supported mainly by a paternal additive effect and revealed possible pleiotropic effects. Based on the grapevine reference genome, we identified 1,173 genes located under these QTL confidence intervals. Fifty of the 891 annotated genes of this list were selected for their further characterisation because of their possible participation in the rachis architecture. In conclusion, the QTLs detected indicate that these traits and their GA₃ responsiveness have a clear genetic basis. Due to the percentage of the total variance explained, they are good candidates to participate in the genetic determination of the cluster architecture.     

Genetic dissection of early-season cold tolerance in sorghum: genome-wide association studies for seedling emergence and survival under field and controlled environment conditions

Key message

A QTL on sorghum chromosome SBI-06 putatively improves field emergence under low-temperature conditions.

Abstract

Low temperatures decisively limit seedling emergence and vigor during early growth of sorghum and, thus, strongly impair geographical expansion. To broaden sorghum cultivation to temperate regions, the establishment of cold-tolerant genotypes is a prioritized breeding goal. The present study aims at the quantification of seedling emergence and survival under chilling temperatures and the detection of marker–trait associations controlling temperature-related seedling establishment. A diversity set consisting of 194 biomass sorghum lines was subjected to extensive phenotyping comprising field trials and controlled environment experiments. The final emergence percentage (FEP) under field conditions was significantly reduced under cold stress. Broad-sense heritability was h ² = 0.87 for FEP in the field and h ² = 0.93 for seedling survival rate (SR) under controlled conditions. Correlations between FEP in the field and under controlled conditions were low; higher correlations were observed between field FEP and SR in controlled environments. Genome-wide association studies (GWAS) were conducted using 44,515 single nucleotide polymorphisms (SNPs) and revealed eight regions with suggestive marker–trait associations for FEP and SR on chromosomes SBI-01, -02, -03, -06, -09, and -10 (p < 5.7 × 10^?5) and a significant association on SBI-06 for field FEP (p < 2.9 × 10^?6). Although not significant under controlled conditions, SR of genotypes carrying the minor allele on the field FEP quantitative trait loci (QTL) on SBI-06 was on average 13.1% higher, while FEP under controlled conditions was on average 9.7% higher with a linearly decreasing effect with increasing temperatures (R ² = 0.82). Promising candidate genes putatively conferring seedling cold tolerance were identified.

     

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

Background

Sorghum (Sorghum bicolor) is globally produced as a source of food, feed, fiber and fuel. Grain and sweet sorghums differ in a number of important traits, including stem sugar and juice accumulation, plant height as well as grain and biomass production. The first whole genome sequence of a grain sorghum is available, but additional genome sequences are required to study genome-wide and intraspecific variation for dissecting the genetic basis of these important traits and for tailor-designed breeding of this important C₄ crop.

Results

We resequenced two sweet and one grain sorghum inbred lines, and identified a set of nearly 1,500 genes differentiating sweet and grain sorghum. These genes fall into ten major metabolic pathways involved in sugar and starch metabolisms, lignin and coumarin biosynthesis, nucleic acid metabolism, stress responses and DNA damage repair. In addition, we uncovered 1,057,018 SNPs, 99,948 indels of 1 to 10 bp in length and 16,487 presence/absence variations as well as 17,111 copy number variations. The majority of the large-effect SNPs, indels and presence/absence variations resided in the genes containing leucine rich repeats, PPR repeats and disease resistance R genes possessing diverse biological functions or under diversifying selection, but were absent in genes that are essential for life.

Conclusions

This is a first report of the identification of genome-wide patterns of genetic variation in sorghum. High-density SNP and indel markers reported here will be a valuable resource for future gene-phenotype studies and the molecular breeding of this important crop and related species.     

Quantitative trait loci of stripe rust resistance in wheat

Key message

Over 140 QTLs for resistance to stripe rust in wheat have been published and through mapping flanking markers on consensus maps, 49 chromosomal regions are identified.

Abstract

Over thirty publications during the last 10 years have identified more than 140 QTLs for stripe rust resistance in wheat. It is likely that many of these QTLs are identical genes that have been spread through plant breeding into diverse backgrounds through phenotypic selection under stripe rust epidemics. Allelism testing can be used to differentiate genes in similar locations but in different genetic backgrounds; however, this is problematic for QTL studies where multiple loci segregate from any one parent. This review utilizes consensus maps to illustrate important genomic regions that have had effects against stripe rust in wheat, and although this methodology cannot distinguish alleles from closely linked genes, it does highlight the extent of genetic diversity for this trait and identifies the most valuable loci and the parents possessing them for utilization in breeding programs. With the advent of cheaper, high throughput genotyping technologies, it is envisioned that there will be many more publications in the near future describing ever more QTLs. This review sets the scene for the coming influx of data and will quickly enable researchers to identify new loci in their given populations.     

Genetic dissection of sorghum grain quality traits using diverse and segregating populations

Key message

Coordinated association and linkage mapping identified 25 grain quality QTLs in multiple environments, and fine mapping of the Wx locus supports the use of high-density genetic markers in linkage mapping.

Abstract

There is a wide range of end-use products made from cereal grains, and these products often demand different grain characteristics. Fortunately, cereal crop species including sorghum [Sorghum bicolor (L.) Moench] contain high phenotypic variation for traits influencing grain quality. Identifying genetic variants underlying this phenotypic variation allows plant breeders to develop genotypes with grain attributes optimized for their intended usage. Multiple sorghum mapping populations were rigorously phenotyped across two environments (SC Coastal Plain and Central TX) in 2 years for five major grain quality traits: amylose, starch, crude protein, crude fat, and gross energy. Coordinated association and linkage mapping revealed several robust QTLs that make prime targets to improve grain quality for food, feed, and fuel products. Although the amylose QTL interval spanned many megabases, the marker with greatest significance was located just 12 kb from waxy (Wx), the primary gene regulating amylose production in cereal grains. This suggests higher resolution mapping in recombinant inbred line (RIL) populations can be obtained when genotyped at a high marker density. The major QTL for crude fat content, identified in both a RIL population and grain sorghum diversity panel, encompassed the DGAT1 locus, a critical gene involved in maize lipid biosynthesis. Another QTL on chromosome 1 was consistently mapped in both RIL populations for multiple grain quality traits including starch, crude protein, and gross energy. Collectively, these genetic regions offer excellent opportunities to manipulate grain composition and set up future studies for gene validation.

     

Development of a genetic linkage map for Pinus radiata and detection of pitch canker disease resistance associated QTLs

Key message

The heritability of genetic resistance of radiata pine against Fusarium circinatum was not clear. We demonstrated that there are at least 3 QTLs that could be involved in this resistance/susceptibility.

Abstract

A genetic linkage map was developed for Pinus radiata, using Amplified Fragment Length Polymorphism (AFLP), Inter-Simple Sequence Repeat (ISSR), Selective Amplification of Microsatellite Polymorphic Loci (SAMPL), and Simple Sequence Repeat (SSR) molecular markers, based on a two-way pseudo-testcross strategy, using 86 individuals of a F1 full-sib family and 787 molecular markers for genotyping. Linkage analysis generated a map of medium to high density for each parent, with 1,060 and 1,258 cM for parents XO and XP, respectively. A total of 458 markers were mapped on 12 linkage groups (LG) in XO and XP, which equals the number of haploid chromosomes present in P. radiata. Analysis of quantitative trait loci (QTL) for resistance against pitch canker disease caused by Fusarium circinatum was made using Bayesian Information Criterion (BIC). In the XO parental map, two groups (LG-1 and LG-9) showed high probabilities for one or more QTLs. Only one group (LG-9) in the XP parental map showed probability for one or more QTLs. The results indicate that resistance to pitch canker is inherited from both parents. These results provide the basis for further studies focused on structure, evolution, and function of the P. radiata genome.     

QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering

Key message

A QTL model for the genetic control of tillering in sorghum is proposed, presenting new opportunities for sorghum breeders to select germplasm with tillering characteristics appropriate for their target environments.

Abstract

Tillering in sorghum can be associated with either the carbon supply–demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum.     

Chemistry and Microbial Functional Diversity Differences in Biofuel Crop and Grassland Soils in Multiple Geographies

We obtained soil samples from geographically diverse switchgrass (Panicum virgatum L.) and sorghum (Sorghum bicolor L.) crop sites and from nearby reference grasslands and compared their edaphic properties, microbial gene diversity and abundance, and active microbial biomass content. We hypothesized that soils under switchgrass, a perennial, would be more similar to reference grassland soils than sorghum, an annual crop. Sorghum crop soils had significantly higher NO₃ ^? -N, NH₄ ⁺ -N, SO₄ ^2? -S, and Cu levels than grassland soils. In contrast, few significant differences in soil chemistry were observed between switchgrass crop and grassland soils. Active bacterial biomass was significantly lower in sorghum soils than switchgrass soils. Using GeoChip 4.0 functional gene arrays, we observed that microbial gene diversity was significantly lower in sorghum soils than grassland soils. Gene diversity at sorghum locations was negatively correlated with NO₃ ^? -N, NH₄ ⁺ -N, and SO₄ ^2? -S in C and N cycling microbial gene categories. Microbial gene diversity at switchgrass sites varied among geographic locations, but crop and grassland sites tended to be similar. Microbial gene abundance did not differ between sorghum crop and grassland soils, but was generally lower in switchgrass crop soils compared to grassland soils. Our results suggest that switchgrass has fewer adverse impacts on microbial soil ecosystem services than cultivation of an annual biofuel crop such as sorghum. Multi-year, multi-disciplinary regional studies comparing these and additional annual and perennial biofuel crop and grassland soils are recommended to help define sustainable crop production and soil ecosystem service practices.     

QTL mapping for resistance to Ceratocystis wilt in <Emphasis Type="Italic">Eucalyptus</Emphasis>

Ceratocystis wilt caused by the fungus Ceratocystis fimbriata, is currently one of the major diseases in commercial plantations of Eucalyptus trees in Brazil. Deployment of resistant genotypes has been the main strategy for effective disease management. The present study aimed at identifying genomic regions underlying the genetic control of resistance to Ceratocystis wilt in Eucalyptus by quantitative trait loci (QTL) mapping in an outbred hybrid progeny derived from a cross between (Eucalyptus dunnii × Eucalyptus grandis) × (Eucalyptus urophylla × Eucalyptus globulus). A segregating population of 127 individuals was phenotyped for resistance to Ceratocystis wilt using controlled inoculation under a completely randomized design with five clonal replicates per individual plant. The phenotypic resistance response followed a continuous variation, enabling us to analyze the trait in a quantitative manner. The population was genotyped with 114 microsatellite markers and 110 were mapped with an average interval of 12.3 cM. Using a sib-pair interval-mapping approach five QTLs were identified for disease resistance, located on linkage groups 1, 3, 5, 8, and 10, and their estimated individual heritability ranged from 0.096 to 0.342. The QTL on linkage group 3 overlaps with other fungal disease-resistance QTLs mapped earlier and is consistent with the annotation of several disease-resistance genes on this chromosome in the E. grandis genome. This is the first study to identify and attempt to quantify the effects of QTLs associated with resistance to Ceratocystis wilt in Eucalyptus.     

Prospecting sugarcane resistance to Sugarcane yellow leaf virus by genome-wide association

Key message

Using GWAS approaches, we detected independent resistant markers in sugarcane towards a vectored virus disease. Based on comparative genomics, several candidate genes potentially involved in virus/aphid/plant interactions were pinpointed.

Abstract

Yellow leaf of sugarcane is an emerging viral disease whose causal agent is a Polerovirus, the Sugarcane yellow leaf virus (SCYLV) transmitted by aphids. To identify quantitative trait loci controlling resistance to yellow leaf which are of direct relevance for breeding, we undertook a genome-wide association study (GWAS) on a sugarcane cultivar panel (n = 189) representative of current breeding germplasm. This panel was fingerprinted with 3,949 polymorphic markers (DArT and AFLP). The panel was phenotyped for SCYLV infection in leaves and stalks in two trials for two crop cycles, under natural disease pressure prevalent in Guadeloupe. Mixed linear models including co-factors representing population structure fixed effects and pairwise kinship random effects provided an efficient control of the risk of inflated type-I error at a genome-wide level. Six independent markers were significantly detected in association with SCYLV resistance phenotype. These markers explained individually between 9 and 14 % of the disease variation of the cultivar panel. Their frequency in the panel was relatively low (8–20 %). Among them, two markers were detected repeatedly across the GWAS exercises based on the different disease resistance parameters. These two markers could be blasted on Sorghum bicolor genome and candidate genes potentially involved in plant–aphid or plant–virus interactions were localized in the vicinity of sorghum homologs of sugarcane markers. Our results illustrate the potential of GWAS approaches to prospect among sugarcane germplasm for accessions likely bearing resistance alleles of significant effect useful in breeding programs.     

The effect of pyramiding two potato cyst nematode resistance loci to Globodera pallida Pa2/3 in potato

Globodera pallida is a major nematode pest causing severe constraints in many potato production regions worldwide. The most prevalent G. pallida pathotypes are Pa2 and Pa3, which exist in mixed populations referred to as Pa2/3. Due to heterogeneity for avirulence genes within these nematode populations, so far, breeders have failed to identify a single resistance gene source which offers complete resistance. Currently, there are two quantitative trait loci (QTL) available, $ GpaIV_{adg}^{s} $ and Gpa5, conferring partial levels of resistance to G. pallida pathotype Pa2/3. The objective of this research was to pyramid $ GpaIV_{adg}^{s} $ and Gpa5 through marker-assisted selection to investigate whether or not pyramiding provides increased resistance to G. pallida Pa2/3. We developed a population segregating for both resistance QTLs and, using diagnostic genetic markers (Contig237 and HC), we identified groups of individuals from this population containing each individual QTL, both QTLs simultaneously, and neither QTL. These individuals were assessed for their resistance levels against G. pallida Pa2/3 population Chavornay. We demonstrated that individuals carrying both QTLs showed a significant reduction in the number of cysts formed in comparison to genotypes carrying $ GpaIV_{adg}^{s} $ or Gpa5, indicating an additive effect. Overall these results show that MAS-based pyramiding of these QTLs is an effective strategy for breeding cultivars exhibiting very high levels of resistance to G. pallida pathotype Pa2/3.     

Genetic architecture of aerial and root traits in field-grown grafted grapevines is largely independent

Key message

QTLs were identified for traits assessed on field-grown grafted grapevines. Root number and section had the largest phenotypic variance explained. Genetic control of root and aerial traits was independent.

Abstract

Breeding new rootstocks for perennial crops remains challenging, mainly because of the number of desirable traits which have to be combined, these traits include good rooting ability and root development. Consequently, the present study analyzes the genetic architecture of root traits in grapevine. A segregating progeny of 138 F1 genotypes issued from an inter-specific cross between Vitis vinifera cv. Cabernet-Sauvignon × V. riparia cv. Gloire de Montpellier, used as rootstock, was phenotyped in grafted plants grown for 2 years in the field. Seven traits, related to aerial and root development, were quantified. Heritability ranged between 0.44 for aerial biomass to 0.7 for root number. Total root number was related to the number of fine roots, while root biomass was related to the number of coarse roots. Significant quantitative trait loci (QTLs) were identified for all the traits studied with some of them explaining approximately 20% of phenotypic variance. Only a single QTL co-localized for root and aerial biomass. Identified QTLs for aerial-to-root biomass ratio suggest that aerial and root traits are controlled independently. Genes known to be involved in auxin signaling pathways and phosphorus nutrition, whose orthologues were previously shown to regulate root development in Arabidopsis, were located in the confidence intervals of several QTLs. This study opens new perspectives for breeding rootstocks with improved root development capacities.