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A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping. Key words: Brassica rapa, morphotypes, structure, alleles, association mapping, doubled haploids. Une collection de 239 accessions du Brassica rapa composee de deux collections nuckeaires representant les differents types morphologiques de diverses origines geographiques est deecrite et son utilisation en analyse d'association est illustree avec la date de floraison. Les auteurs ont analyse; la variation pheenotypique pour des caracteres de la feuille et de la silique, la forme de la plante et la date de floraison en utilisant les donneees recueillies lors de trois experiences au champ et evaluee la diversite genetique avec un jeu de marqueurs SSR. Les collections nuckeaires de Wageningen (WUR) et de Vavilov (VIR) comptaient des nombres comparables de la plupart des types morphologiques, tel qu'illustre par la variation pheenotypique et genetique au sein de ces groupes. L'analyse de la structure de la population a reveke l'existence de cinq sous-groupes au sein de la collection, tandis que les etudes anterieures de la collection WUR avaient suggere la presencedequatresous-groupes. Lecinquieme groupe identifie etait compose principalement d'accessions oleagineuses de la collection VIR, d'oleagineux d'automne du Pakistan et de quelques autres types. Un tres petit groupe d'oleagineux de printemps, sans lien avec les autres accessions d'oleagineux, est deecrit. Une approche faisant appel a des genes candidats a ete choisie pour l'analyse d'association avec la date de floraison. Un marqueur CAPS biallelique pour le gene BrFLC1 et un marqueur SSR multiallelique pour le gene BrFLC2 ont ete employes. Les deux marqueurs etaient significativement assockesa la date de floraison, mais leurs effets etaient limitesa certains types morphologiques ou alleles. Surla basedeces resultats, les auteurs discutent de la composition optimale d'une population pour l'analyse d'association et de la necessite de fixer les accessions heterogenes pour faciliter le phenotypage et le geenotypage. Mots-cles : Brassica rapa, types morphologiques, structure, alleles, analyse d'association, haploides doubles. [Traduit par la Redaction], Introduction The genus Brassica has a long history of world wide cultivation, and cultivated Brassica species comprises a large and diverse group of important vegetable, oil, fodder, and condiment crops. [...]

Cassava green mite [CGM, Mononychellus tanajoa (Bondar)] is a dry-season pest that usually feeds on the underside of young leaves causing leaf chlorosis, stunted growth, and root yield reduction by 80%. Since cassava (Manihot esculenta Crantz) leaves and roots serve as a primary staple food source, a decline in cassava yield can lead to household food, nutrition, and income insecurity. To evaluate the existence of CGM resistance alleles in the available germplasm, a diversity panel of 845 advanced breeding lines obtained from IITA, CIAT, and the National Root Crops Research Institute (NRCRI) were evaluated for CGM severity (CGMS), leaf pubescence (LP), leaf retention (LR), stay green, shoot tip compactness, and shoot tip size. A genome-wide association mapping detected 35 single-nucleotide polymorphisms (SNPs) markers significantly associated with CGMS, LP, and LR on chromosome 8. Colocalization of the most significant SNP associated with CGMS, LP, and LR on chromosome 8 is possibly an indication of pleiotropy or the presence of closely linked genes that regulate these traits. Seventeen candidate genes were found to be associated to CGM resistance. These candidate genes were subdivided into seven categories according to their protein structure namely, Zn finger, pentatricopeptide, MYB, MADS, homeodomain, trichome birefringence-related protein, and ethylene-responsive transcription factor genes. This study revealed significant loci associated with CGM, not previously reported, which together represent potential sources for the ongoing effort to develop multiple pest- and disease-resistant cassava cultivars. [ABSTRACT FROM AUTHOR]

• Glucosinolates and their breakdown products have been recognized for their effects on plant defense, human health, flavor and taste of cruciferous vegetables. Despite this importance, little is known about the regulation of the biosynthesis and degradation in Brassica rapa. • Here, the identification of quantitative trait loci (QTL) for glucosinolate accumulation in B. rapa leaves in two novel segregating double haploid (DH) populations is reported: DH38, derived from a cross between yellow sarson R500 and pak choi variety HK Naibaicai; and DH30, from a cross between yellow sarson R500 and Kairyou Hakata, a Japanese vegetable turnip variety. • An integrated map of 1068 cM with 10 linkage groups, assigned to the international agreed nomenclature, is developed based on the two individual DH maps with the common parent using amplified fragment length polymorphism (AFLP) and single sequence repeat (SSR) markers. Eight different glucosinolate compounds were detected in parents and F1s of the DH populations and found to segregate quantitatively in the DH populations. QTL analysis identified 16 loci controlling aliphatic glucosinolate accumulation, three loci controlling total indolic glucosinolate concentration and three loci regulating aromatic glucosinolate concentrations. • Both comparative genomic analyses based on Arabidopsis– Brassica rapa synteny and mapping of candidate orthologous genes in B. rapa allowed the selection of genes involved in the glucosinolate biosynthesis pathway that may account for the identified QTL. [ABSTRACT FROM AUTHOR]

Wide variation for morphological traits exists in Brassica rapa and the genetic basis of this morphological variation is largely unknown. Here is a report on quantitative trait loci (QTL) analysis of flowering time, seed and pod traits, growth-related traits, leaf morphology, and turnip formation in B. rapa using multiple populations. The populations resulted from crosses between the following accessions: Rapid cycling, Chinese cabbage, Yellow sarson, Pak choi, and a Japanese vegetable turnip variety. A total of 27 QTL affecting 20 morphological traits were detected, including eight QTL for flowering time, six for seed traits, three for growth-related traits and 10 for leaf traits. One major QTL was found for turnip formation. Principal component analysis and co-localization of QTL indicated that some loci controlling leaf and seed-related traits and those for flowering time and turnip formation might be the same. The major flowering time QTL detected in all populations on linkage group R02 co-localized with BrFLC2. One major QTL, controlling turnip formation, was also mapped at this locus. The genes that may underly this QTL and comparative analyses between the four populations and with Arabidopsis thaliana are discussed. [ABSTRACT FROM PUBLISHER]

Control of gene expression is fundamental at every level of cell function. Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have only been studied in a handful of research experiments in plants. PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally engaged RNA polymerase at both the 5' and 3' end of genes, consistent with paused or slowly moving Polymerase. In addition, we identified divergent transcription at intergenic sites. A full genome search for bi-directional transcription using an algorithm for enhancer detection developed in mammals (dREG) identified many intergenic regulatory element (IRE) candidates. These sites showed distinct patterns of methylation and nucleotide conservation based on genomic evolutionary rate profiling (GERP). SNPs within these IRE candidates explained significantly more variation in fitness and root composition than SNPs in chromosomal segments randomly ascertained from the same intergenic distribution, strongly suggesting a functional importance of these sites. Maize GRO-Seq data showed RNA polymerase occupancy at IREs consistent with patterns in cassava. Furthermore, these IREs in maize significantly overlapped with sites previously identified on the basis of open chromatin, histone marks, and methylation, and were enriched for reported eQTL. Our results suggest that bidirectional transcription can identify intergenic genomic regions in plants that play an important role in transcription regulation and whose identification has the potential to aid crop improvement., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)