Genetic analysis of resistance to bacterial leaf spot in the heirloom lettuce cultivar Reine des Glaces Abstract Bacterial leaf spot (BLS) is a disease that affects lettuce (Lactuca sativa L.) worldwide. The disease is caused by the bacterium Xanthomonas campestris pathovar vitians (Xcv), which exclusively infects lettuce and is particularly devastating in warm humid climates. Reine des Glaces (RG), an old Batavia-type cultivar, exhibited an uninvestigated partial resistance to Xcv. Quantitative trait loci (QTLs) were analyzed using two recombinant inbred line (RIL) populations derived from RG × Eruption and RG × Delsay using three isolates collected in California and Canada, each representing a different race, and an isolate collected in France. A major QTL was identified in linkage group 2 in both populations; additional, minor QTLs were also detected in other linkage groups. The major QTL collocates with the Xanthomonas resistance 1 (Xar1) and Xanthomonas campestris vitians resistance (Xcvr) genes that had previously been identified using RIL populations derived from Salinas 88 × La Brillante and PI 358001-1 × Tall Guzmaine. RG provides another resistance resource for combating BLS using data provided by this study for marker-assisted selection.

Current understanding of genetic and molecular basis of cold tolerance in rice Abstract Rice (Oryza sativa L.) is one of the most important crops worldwide, but its growth and production can be severely affected by climate change. As a tropical species, rice is in general vulnerable to the adverse effects of low temperature. To cope with or adapt to cold stress condition, rice has evolved elaborate regulatory mechanisms under both natural and artificial selection. Over the past few decades, intensive research efforts have been focused on abiotic stress biology in rice with genetic, genomic, and molecular strategies, disclosing a series of potential genetic determinants and mechanisms controlling cold stress tolerance. Here, we review cold tolerance (CT)-related quantitative trait loci (QTLs) identified by linkage and association mapping, together with key genes involved in cold sensing, signaling, and response. More importantly, recent studies have shown that CT-related QTLs/genes can be employed in genomic breeding aiming at developing cold-tolerant rice. Overall, the recent research progresses in understanding the complex genetic and molecular mechanisms of CT provide a substantial basis for CT improvement in rice.

Dissecting the genetic architecture of important traits that enhance wild germplasm resource usage in modern maize breeding Abstract Domestication and improvement of maize (Zea mays L.) from ~ 10,000 years ago has produced remarkable alterations from its wild ancestor, teosinte. To investigate the genetic basis of changes in plant and inflorescence traits, we developed a teosinte–maize intermated population. More than 200 common quantitative trait loci (QTLs) and 44 QTL clusters were identified underlying 13 vegetative and reproductive traits. Among them, few common QTLs with major effects were observed, which supported previous hypotheses that a small number of major loci can explain a large portion of phenotypic changes during domestication. Additionally, we found many moderate or minor QTLs that might have critical roles in shaping plant architecture and enhancing grain yield of modern maize. Although maize has better performance for the traits studied here, teosinte still harbored desirable alleles in some of the common QTLs. Furthermore, we integrated multiple datasets and predicted candidate genes underlying these QTLs. This study elucidates the genetic basis of these vegetative and reproductive traits in maize and teosinte, and suggests the possibility of improving maize by teosinte re-domestication using a small number of loci.

Peptidomics-based study reveals that GAPEP1, a novel small peptide derived from pathogenesis-related (PR) protein of cotton, enhances fungal disease resistance Abstract Peptides play important roles in many important biological processes. For instance, plant antimicrobial peptides, which are essential components of innate immunity and exert rapid defense response, have a broad activity against pathogenic bacteria, fungi, enveloped viruses, and parasites. Verticillium wilt, caused by the soil-borne fungus Verticillium dahliae, is a destructive vascular disease in plants. In this study, we used mass spectrometry approach to detect and characterize important peptides, especially antimicrobial peptides from roots of Gossypium arboretum and to evaluate their inhibitory activities against phytopathogenic fungi. We have identified a novel small peptide, GAPEP1, which is derived from the N-terminal of Pathogenesis-related protein STH-2 protein and upregulated by V. dahliae inoculation. GAPEP1 is localized in the nucleus and cell membrane. Plants with exogenous treatment or overexpressing GAPEP1 both exhibited enhanced disease resistance as compared with the control group. Our results provide the cotton endogenous peptides library that could potentially be used to develop natural, targeted, and environmentally friendly strategies to enhance the resistance of Gossypium species against biotic attackers.

Transcriptome analysis reveals genes commonly responding to multiple abiotic stresses in rapeseed Abstract Rapeseed production is limited by abiotic stresses such as drought, salinity, and low temperature. Evidences suggest that common stress response genes are shared by multiple stresses. To study how rapeseed responds to abiotic stresses at transcriptional level and identify genes that regulate multiple abiotic stress tolerance, we investigated transcriptional dynamics of the rapeseed treated by abscisic acid (ABA), salt, dehydration, and cold stresses at two different time points, respectively. A total of 30,908 differentially expressed genes (DEGs) under 4 abiotic stresses were identified. There were 2568 upregulated and 4376 downregulated DEGs (2-fold change) commonly shared by four stresses. Analysis of the DEGs identified significantly enriched gene ontology biological processes under multiple stress conditions. The commonly shared DEGs included 225 upregulated and 294 downregulated transcription factors belonging to 35 and 40 different families, respectively. The representative mostly upregulated and downregulated DEGs at each time point of abiotic stress treatment were presented. We identified a list of core abiotic stress genes commonly regulated by four stresses, which mainly included ERD15, RAB18, LEA14, and transcription factors belonging to ERF, bZIP, and MYBR1 families. The findings of shared abiotic stress responsive genes may help develop strategies for breeding rapeseed varieties with improved tolerance to multiple abiotic stresses.

Basmati rice lines development carrying multiple bacterial blight resistance genes pyramided using the marker-assisted backcross breeding approach Abstract Basmati rice is treated as one of the world’s best rice due to its extra-long grain and unique aroma,. Over the last decade, Pakistan has earned more than US$2 billion through basmati export. Unfortunately, basmati rice is being threatened with bacterial leaf blight (BLB) disease that leads to poor production and quality. We attempted pyramiding of BLB genes through marker-assisted backcross breeding using Super Basmati as the recipient and IRBB60 as the donor parent. BLB resistance genes Xa4, xa5, and Xa21 were used for introgression. Molecular markers MP1 and MP2, RM122, and pTA248 were used for Xa4, xa5, and Xa21 genes respectively for foreground selection. The 85 SSR polymorphic molecular markers were used for background selection, which showed a more than 90% recurrent parent genome recovery. Phenotypic traits for grain dimensions were also considered while selecting backcross female parents from BC1F1 to BC5F1, which resulted in saving the resources from background selection before the selfing of backcrossed lines. Multiple lines carrying BLB resistance genes combinations Xa4 + xa5 and Xa4 + xa5 + Xa21 were developed. The BC5F4 uniform lines showed resistance against BLB disease at hotspot locations. One of the developed lines, PKBB15–116, which has a yield advantage of more than 10%, tolerant to lodging, and has basmati quality. These pyramided lines in basmati background will also be helpful for breeders to incorporate resistance genes in a shorter period of time, in order to develop new basmati rice varieties in future.

An update on molecular mechanism of disease resistance genes and their application for genetic improvement of rice Abstract Multiple pathogens cause rice various diseases affecting its yield and quality. Pyramiding resistance genes or quantitative traits loci into rice cultivars to enhance their resistance is an operable and optimal strategy for rice genetic improvement. New technologies and methods accelerate the identification and cloning of the resistance genes from landraces, domesticated and wild rice germplasm accessions. Some of these superior resistance genes have been successfully pyramided into diverse rice cultivars worldwide based on molecular marker-assisted selection. The underlying molecular mechanisms of some resistance genes have been uncovered which support their stacking into rice cultivars in a proper manner. The genetically improved rice lines show broad spectrum and durable resistance to different pathogens, which can greatly contribute to high yield and outstanding quality of rice cultivars. This paper summarizes the cloned major resistance genes, elucidates the underlying molecular mechanisms, and proposes the operable strategies to use these genes for rice genetic improvement.

Genetic variation analysis of field isolates of clubroot and their responses to Brassica napus lines containing resistant genes CRb and PbBa8.1 and their combination in homozygous and heterozygous state Abstract Brassica napus is one of the most important oilseed crops in the world and Plasmodiophora brassicae is a serious threat causing yield reduction. CRb and PbBa8.1 resistance genes are known to be highly effective against P. brassicae race 4. Here, we combined two clubroot resistance (CR) genes through marker-assisted selection (MAS) and developed CR homozygous lines. The CR parental and pyramided lines were crossed with genetically male sterile (GMS) plants to generate heterozygous lines. In order to confirm their differences on resistance, the parental and generated lines were inoculated with 9 P. brassicae field isolates in the greenhouse and resistant test also evaluated in different naturally infested fields. The CR pyramiding lines exhibited high levels of resistance to the most isolates than line containing any single resistance gene; comparatively, the homozygous lines demonstrated a higher resistance than the heterozygous. The genetic variation among P. brassicae isolates was analyzed through simple sequence repeat (SSR) marker and significant divergences were recorded among the 9 tested field isolates and the result was consistent with data acquired from the greenhouse and natural field experiments. This study will certainly provide a novel molecular strategy for the breeding of the durable CR B. napus varieties in future breeding programs.

Multi-environments and multi-models association mapping identified candidate genes of lint percentage and seed index in Gossypium hirsutum L. Abstract Upland cotton (Gossypium hirsutum L.) accounts most of the natural fiber production worldwide. Lint percentage (LP) and seed index (SI) are important components of cotton fiber yield, which is a constant breeding goal of cotton. So, the loci underpinning LP and SI should be extensively dissected. Here, one single-locus and four multi-locus genome-wide association study (GWAS) models were employed to detect candidate loci for lint percentage and seed index under seven environments with 196 upland cotton accessions and 41,815 single nucleotide polymorphism (SNP) markers. Totally, 39 and 45 significant quantitative trait locus (QTL) were identified in at least two environments or two models, including 24 previously reported QTLs and six pleiotropic QTLs. Referred to the genome and gene expression database of TM-1, 614 candidate genes were detected for lint percentage and seed index, including 103 genes preferentially expressed in fiber or ovule. The gene Gh_A10G0378, functioned in potassium ion transport, was considered to be related to lint percentage. Collectively, the associated markers and promising genes detected herein will help to elucidate the genetic architecture of lint percentage and facilitate fiber yield improvement in cotton.

Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content Abstract Valorisation of tuber protein is relevant for the potato starch industry to create added-value and reduce impact on the environment. Hence, protein content has emerged as a key quality trait for innovative potato breeders. In this study, we estimated trait heritability, explored the relationship between protein content and tuber under-water weight (UWW), inferred haplotypes underlying quantitative trait loci (QTLs) and pinpointed candidate genes. We used a panel of varieties (N = 277) that was genotyped using the SolSTW 20 K Infinium single-nucleotide polymorphism (SNP) marker array. Protein content data were collected from multiple environments and years. Our genome-wide association study (GWAS) identified QTLs on chromosomes 3, 5, 7 and 12. Alleles of StCDF1 (maturity) were associated with QTLs found on chromosome 5. The QTLs on chromosomes 7 and 12 are presented here for the first time, whereas those on chromosomes 3 and 5 co-localized with loci reported in earlier studies. The candidate genes underlying the QTLs proposed here are relevant for functional studies. This study provides resources for genomics-enabled breeding for protein content in potato.