Identification of novel genetic regions associated with resistance to European canker in apple

Resistance to Neonectria ditissima, the fungus causing European canker in apple, was studied in a multiparental population of apple scions using several phenotyping methods. The studied population consists of individuals from multiple families connected through a common pedigree. The degree of disease of each individual in the population was assessed in three experiments: artificial inoculations of detached dormant shoots, potted trees in a glasshouse and in a replicated field experiment. The genetic basis of the differences in disease was studied using a pedigree-based analysis (PBA). Three quantitative trait loci (QTL), on linkage groups (LG) 6, 8 and 10 were identified in more than one of the phenotyping strategies. An additional four QTL, on LG 2, 5, 15 and 16 were only identified in the field experiment. The QTL on LG2 and 16 were further validated in a biparental population. QTL effect sizes were small to moderate with 4.3 to 19 % of variance explained by a single QTL. A subsequent analysis of QTL haplotypes revealed a dynamic response to this disease, in which the estimated effect of a haplotype varied over the field time-points. Two groups of QTL-haplotypes could be distinguished, one that displayed increased effect and one with a constant effect across time-points. These results suggest that there are different modes of control of N. ditissima in the early stages of infection compared to later time-points of disease development. It also shows that multiple QTL will need to be considered to improve resistance to European canker in apple breeding germplasm.

Advanced Yield Trial for Various Peanut Lines (Arachis hypogaea L.) at Sodonghilir, Tasikmalaya, West Java, Indonesia

This study aims to evaluate yield and yield components in several peanut lines planted in West Java, Indonesia. The genetic materials tested involved 21 genotypes consisting of 18 potential peanut lines (G100, G133, G142, G144, G199, G205, G209, G21, G234, G237, G33, G37, G41, G53, G54, G76, G84, G99) from a selection of 5 biparental population (GWS79A1/”Zebra”, “Jerapah”/GWS79A1, “Zebra”/GWS79A1, GWS79A1/”Jerapah”, “Zebra”/GWS18A1) and 3 comparative varieties (“Gajah”, “Sima”, and “Zebra”) as controls. Results showed that various genotypes have significant effects on plant height (at 9 and 10 WAP), number of branches (at 4, 10, and 12 WAP), flowering age, and harvest age. Some potential lines showed ideal characters expected of a high quality peanut plant. Based on characters such as harvest age, dry pod weight, and productivity, G100, G41, G21, G205, and G84 can be considered the best potential lines. These lines demonstrated high heritability values including characters classified as high category such as plant height, number of branches, age of flowering, age of harvest, harvest index, wet stover weight, fresh pod weight, number of filled pods, number of empty pods, number of filled pods, and weight of 100 seeds. Additionally, these lines also show high productivity, a character classified in the medium category.

Selection of F2 homozygous plants over the QTL9 related to rice panicle structure by using CAPS markers

QTL9 is a new potential quantitative trait locus related to rice panicle structure, identified through a GWAS analysis of Vietnamese local rice panel. To validate the QTL9, a biparental population was developed using the low branching (G6) and the high branching (G189) accessions from two haplotypes characterised by a contrasting phenotype for the secondary branch number and spikelet number traits. In parallel, using Gene capture technology combined with new generation sequencing identified 1,002 genetic variants in the QTL9 region between two parents, of which 12 SNPs were found in the cleavage site of 5 restriction enzyme. In this study, 12 primer pairs were tested to amplify the CAPS markers, based on the 12 SNPs, in order to be applied to select homozygous F2 lines over the QTL9 region for both haplotypes. 4 CAPS markers were selected distributing over the QTL9 region and displaying polymorphism between two parents. 275 F2plants were genotyped using 3 CAPS markers leading to the selection of 74 homozygotes plants over the QTL9region for haplotype 1, 66 homozygotes plants over the QTL9 region for haplotype 2, and 153 heterozygous plants. Homozygous lines will be used to develop the F3population, phenotyping of two F3 haplotypes will lead to discovering the role of QTL9 related to rice panicle structure.

Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean

Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency.

QTL identification for nine seed-related traits in Brassica juncea using a multiparent advanced generation intercross (MAGIC) population

Agronomic traits are usually determined by multiple quantitative trait loci (QTLs) that can have pleiotropic effects. A multiparent advanced generation intercross (MAGIC) population is well suited for genetically analysing the effects of multiple QTLs on the traits of interest because it contains more QTL alleles than a biparental population and can overcome the problem of confounding the population structure of the natural germplasm population. We previously developed the B. juncea MAGIC population, derived from eight B. juncea lines with great diversity in agronomic and quality traits. In this study, we show that the B. juncea MAGIC population is also effective for the evaluation of multiple QTLs for complex agronomic traits in B. juncea. A total of twenty-two QTLs for nine seed-related traits were identified, including one QTL for each oil content, seed number per silique and thousand-seed weight; two QTLs for each acid detergent lignin and neutral detergent fibre; three QTLs for each acid detergent fibre and protein content; four QTLs for the seed maturity time; and five QTLs for the white index. Some of these QTLs overlapped. These results should be helpful for further fine mapping, gene cloning, plant breeding and marker-assisted selection (MAS) in B. juncea.

Utilization of the Genomewide Wheat 55K SNP Array for Genetic Analysis of Stripe Rust Resistance in Common Wheat Line P9936

Breeding for resistance to stripe rust (caused by Puccinia striiformis f. tritici) is essential for reducing losses in yield and quality in wheat. To identify genes for use in breeding, a biparental population of 186 recombinant inbred lines (RILs) from a cross of the Chinese landrace Mingxian 169 and CIMMYT-derived line P9936 was evaluated in field nurseries either artificially or naturally inoculated in two crop seasons. Each of the RILs and parents was genotyped with the wheat 55K single-nucleotide polymorphism (SNP) ‘Breeders’ array and a genetic linkage map with 8,225 polymorphic SNP markers spanning 3,593.37 centimorgans was constructed. Two major quantitative trait loci (QTL) and two minor QTL were identified. The major QTL QYr.nwafu-3BS.2 and QYr.nwafu-7BL on chromosomes arms 3BS and 7BL were detected in all field locations and explained an average 20.4 and 38.9% of phenotypic variation stripe rust severity, respectively. QYr.nwafu-3BS.2 likely corresponds to the locus Yr30/Sr2 and QYr.nwafu-7BL may be a resistance allele identified previously in CIMMYT germplasm. The other minor QTL had limited individual effects but increased resistance when in combinations with other QTL. Markers linked to QYr.nwafu-7BL were converted to kompetitive allele-specific polymerase chain reaction markers and validated in a panel of wheat accessions. Wheat accessions carrying the same haplotype as P9936 at the identified SNP loci had lower average stripe rust severity than the average severity of all other haplotypes.