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Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.

Tesis llevada a cabo para conseguir el grado de Doctor por la Universidad Autónoma de Barcelona--2016-09-02, [CA] La hibridació és un fenomen molt freqüent en plantes, però els híbrids solen ser estèrils. Existeixen barreres reproductives que dificulten l’intercanvi genètic entre espècies, però, no obstant, aquest acaba tenint lloc. Això genera moltes preguntes, com ara les següents. Quines solen ser aquestes barreres i, sobretot, com aconsegueixen ser superades? Quin paper hi té l’aïllament geogràfic? En zones de muntanya, s’ha proposat la vicariància com a procés clau en la diversificació de les plantes, però realment és la vicariància el procés que contribueix majoritàriament a la diversificació de plantes en els hàbitats de muntanya? L’objectiu d’aquesta tesi és trobar respostes a aquestes preguntes i per això tractarem les diferents qüestions en diversos grups de plantes que s’hi ajusten en base a estudis previs. Els grans temes que abordem amb aquesta idea són els següents: i) processos d’especiació per hibridació en un grup citogenèticament complex d’espècies de muntanya, la secció Triplinervium del gènere Saxifraga (Saxifragaceae), ii) híbrids F1 i el seu tractament taxonòmic: caracterització i tipificació de Jacobaea ×mirabilis (Asteraceae), iii) hibridació i introgressió en endemismes de muntanya, una possible amenaça per a la conservació? Estudi sobre les dues espècies del gènere Rhaponticum (Asteraceae) dels Alps: R. heleniifolium i R. scariosum, i iv) diversificació del gènere Artemisia (Asteraceae) a l’alta muntanya europea: quins són els factors que hi han contribuït de manera més decisiva? Els resultats obtinguts en les diferents publicacions d’aquesta tesi mostren que les principals fonts de diversificació en plantes són l’intercanvi genètic (hibridació i introgressió) i les mutacions cromosòmiques (com guanys, pèrdues o reestructuracions de braços cromosòmics, que poden acabar derivant en casos de disploïdia). Per contra, l’aïllament geogràfic per se no genera diversificació, però permet la fixació de noves combinacions cromosòmiques per processos de coll d’ampolla, o bé facilita o impedeix el contacte entre diferents espècies, és a dir, determina quines espècies poden acabar hibridant. En els casos que hem estudiat, i a diferència del que se sol postular, s’ha pogut constatar, a més, que la poliploïdia no és la font més comuna d’origen de noves espècies, sinó que l’especiació sol tenir lloc en el mateix nivell de ploïdia, ja sigui després d’una hibridació (especiació híbrida homoploide o hibridació introgressiva) o bé per canvi del nombre cromosòmic bàsic (disploïdia), [ES] Hybridization is widespread in plants, but only infrequently results in viable or fertile offspring. There are reproductive barriers, which hamper the genetic exchange between species, but, nevertheless, this ends up taking place. This generates many questions such as the following: What are usually these barriers, and, especially, how do plants achieve to overcome them? What role does geographical isolation play? In mountain regions, vicariance has been proposed as a key process on plants diversification, but is it actually vicariance the process that mainly contributes to plant diversification on mountain habitats? The aim of this thesis is to find answers to these questions, and therefore we will deal the different issues with several plant groups according to previous studies. The major topics addressed with this idea are the following: i) hybrid speciation processes in a cytogenetically complex group of mountain species, section Triplinervium of genus Saxifraga (Saxifragaceae), ii) F1 hybrids and their taxonomic treatment: characterization and typification of Jacobaea ×mirabilis (Asteraceae), iii) hybridization and introgression on mountain endemic plants, a possible threat to conservation? Study about the two alpine species of Rhaponticum genus (Asteraceae): R. heleniifolium and R. scariosum and, iv) diversification of European high mountain Artemisia (Asteraceae): what are the factors that have contributed in the most decisive way? The results obtained in the different publications of this thesis show that the main sources of diversification in plants are genetic exchange (hybridization and introgression) and chromosomic mutations (like gains, losses or chromosome arms restructuration, which can end up to dysploidy cases). Conversely, geographical isolation per se does not generate diversification, but it allows the establishment of new chromosomal combinations by bottleneck processes and/or impedes or facilitates contacts between different species, i.e. determining which species can hybridize. In the cases we studied, unlike what is usually postulated, it has been additionally shown that polyploidy is not the most common source of origin of new species, but rather speciation took place on the same ploidy level, either after hybridization (homoploid hybrid speciation or introgressive hybridization) or by changing the basic chromosome number (dysploidy).

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.

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry.

L'enzim HMG-CoA reductasa (HMGR) catalitza la primera etapa limitant en la síntesi d'isoprenoides citosòlics. En plantes, és un enzim de membrana i la seva primera destinació subcel·lular és el reticle endoplasmàtic. Estructuralment, està formada per un domini amino-terminal (que inclou una regió amino-terminal citosòlica i dos fragments transmembrana) i un domini catalític altament conservat en tota l'escala evolutiva. En totes les espècies de plantes conegudes fins al moment, existeixen isoformes de l'HMGR codificades per diferents gens. Concretament, en Arabidopsis thaliana el gen hmg1 (expressat de forma majoritària) codifica per a les isoformes HMGR1S i HMGR1L, i el gen hmg2 (expressat a arrels, plàntules i inflorescències) codifica per a la isoforma HMGR2. A nivell d'estructura primària l'HMGR1L difereix de l'HMGR1S per la presència d'una regió extra de 50 residus aminoacídics a l'extrem amino-terminal. El domini amino-terminal confereix diferents destinacions de localització subcel·lular a la proteïna. En un treball anterior, es van identificar tres proteïnes que interaccionen amb les isoformes derivades del gen hmg1: AtB"α, AtB"β i AtKLC-1. Les dues primeres interaccionen específicament amb la regió amino-terminal de les isoformes HMGR1S i HMGR1L. Les proteïnes AtB"α i AtB"β són isoformes de la subunitat B" reguladora del complex proteïna fosfatasa 2A (PP2A). En el genoma d'A. thaliana hi ha cinc seqüències que codifiquen per a isoformes de la subunitat B" que comparteixen una gran homologia. En l'estructura primària de la subunitat B" s'han identificat motius EF-Hand (implicats en la unió a calci). S'ha demostrat que tant AtB"α com AtB"β uneixen calci. La tercera proteïna identificada, AtKLC-1, interacciona específicament amb la regió amino-terminal de l'HMGR1L. S'ha determinat per assaigs de doble híbrid en llevat i, posteriorment confirmats in vitro, que la PR65, proteïna estructural del complex PP2A, interacciona específicament amb l'AtKLC-1. La regió de la PR65 suficient per a la interacció amb la subunitat B" reguladora, AtB"α, i amb l'AtKLC-1 comprèn la mateixa seqüència aminoacídica. Per tant, l'AtB"α i l'AtKLC-1 podrien competir per a l'associació amb la PR65. Així, en la cèl·lula, la PP2A podria regular d'una forma particular les isoformes HMGR1S i HMGR1L. Assaigs in vivo i in vitro demostren que la PP2A és un regulador negatiu de l'enzim HMGR. Els ions calci inhibeixen també l'activitat HMGR. Per a què es dugui a terme la repressió de l'activitat HMGR tant per calci com per PP2A, es requereix el domini amino-terminal de la proteïna. Per tant, els resultats són consistents amb què les subunitats AtB" i/o AtKLC-1 duen a terme un paper mediador en la modulació de l'HMGR per la PP2A. El domini amino-terminal de l'HMGR1S està implicat en la morfogènesi de vesícules derivades del reticle endoplasmàtic. La subunitat AtB"α i la resta del complex PP2A participen en aquest procés. El domini amino-terminal de l'HMGR1L dirigeix la proteïna a la trama de reticle endoplasmàtic. La PP2A participa també en la localització subcel·lular d'aquesta isoforma.S'ha caracteritzat una línia mutant en el gen hmg1 d'A. thaliana que mostra absència del transcrit hmg1 i una reduïda activitat HMGR. Les plantes d'aquest mutant creixen normalment en un medi de cultiu estèril i manifesten severes alteracions del desenvolupament quan són cultivades en terra. L'addició de mevalonat, producte de la reacció catalitzada per l'HMGR, no reverteix el fenotip. Les dades indiquen que el gen hmg1 duu a terme una funció no metabòlica relacionada amb l'adaptació al medi. En aquestes condicions de creixement, les estructures vesiculars induïdes per l'HMGR1S podrien tenir alguna funció essencial relacionada amb la resposta a estrès., "ROLE OF THE PROTEINS AtKLC-1 AND AtB" IN THE REGULATION OF HMG-CoA REDUCTASE IN ARABIDOPSIS THALIANA".TEXT: The enzyme HMG-CoA reductase (HMGR) catalyses the formation of mevalonate in the first rate-limiting step of the mevalonate pathway for isoprenoid biosynthesis. All known plant HMGR isoforms are primarily targeted to the endoplasmic reticulum (ER).These proteins contain two domains: an N-terminal domain (which includes an N-terminal cytosolic region and two membrane-spanning sequences) and a conserved catalytic domain. In all plant species, there are a variety of HMGR isoforms encoded by a multigene family. In Arabidopsis thaliana, two genes (hmg1 and hmg2) encode three HMGR isoforms (HMGR1S, HMGR1L and HMGR2). Isoforms HMGR1S and HMGR1L are identical in sequence but HMGR1L is extended 50 amino acid residues at the N-terminal end. In a previous study, three proteins had been identified which specifically interact with the HMGR1L N-terminal end. Two of these proteins, designed AtB" and AtB", are regulatory B" subunits of protein phosphatase 2A (PP2A). They bind the N-terminal region of HMGR1S and HMGR1L. The third one, AtKLC-1, exclusively interact with the N-terminal region of HMGR1L. In vitro assays have revealed that PR65, PP2A scaffolding subunit, specifically interact with AtKLC-1. Genetic and pharmacological approaches demonstrate that PP2A exerts an inhibitory control over HMGR. These results indicate that AtB" or AtKLC-1 could have a mediating role in the HMGR regulation carried out by PP2A. The N-terminal domain of the HMGR1S isoform is involved in the biogenesis of vesicle structures derived from the ER membranes. The PP2A complex is concerned in this process and the subunit AtB" acts as an interceding factor. Furthermore, we have characterized an Arabidopsis thaliana insertion mutant for hmg1. This mutant exhibits no visible phenotype under sterile growth conditions but shows dwarfing and sterility when it is grown in a soil substrate. The addition of mevalonate doesn't rescue this phenotype. These data suggest that hmg1 performs a no-metabolic function related with environment adaptation. In this context, ER derived vesicles induced by HMGR1S could play an essential role related with stress response.

The large daisy tribe Gnaphalieae occurs in extra-tropical habitats worldwide, but is most diverse in southern Africa and in Australia. We explore the age and evolutionary history of the tribe by means of a phylogenetic hypothesis based on Bayesian analysis of plastid and nuclear DNA sequences, maximum likelihood reconstruction of ancestral areas, and relaxed Bayesian dating. Early diversification occurred in southern Africa in the Eocene-Oligocene, resulting in a grade of mostly Cape-centred lineages which subsequently began speciating in the Miocene, consistent with diversification times for many Cape groups. Gnaphalieae from other geographic regions are embedded within a southern African paraphylum, indicating multiple dispersals out of southern Africa since the Oligocene to Miocene which established the tribe in the rest of the world. Colonisation of Australia via direct long-distance trans-oceanic dispersal in the Miocene resulted in the radiation which produced the Australasian gnaphalioid flora. The similarly diverse regional gnaphalioid floras of Australasia and southern Africa thus exhibit very different temporal species accumulation histories. An examination of the timing and direction of trans-Indian Ocean dispersal events in other angiosperms suggests a role for the West Wind Drift in long-distance dispersal eastwards from southern Africa.

Tobacco mosaic virus(TMV) has served as a model organism for pathbreaking work in plant pathology, virology, biochemistry and applied genetics for more than a century. We were intrigued by a photograph published inPhytopathologyin 1934 showing that Tabasco pepper plants responded to TMV infection with localized necrotic lesions, followed by abscission of the inoculated leaves. This dramatic outcome of a biological response to infection observed by Francis O. Holmes, a virologist at the Rockefeller Institute for Medical Research, was used to score plants for resistance to TMV infection. Our objective was to gain a better understanding of early to mid-twentieth century ideas of genetic resistance to viruses in crop plants. We investigated Holmes’ observation as a practical exercise in reworking an experiment, having been inspired by Pamela Smith’s innovative Making and Knowing Project. We had a great deal of difficulty replicating Holmes’ experiment, finding that biological materials and experimental customs change over time, in ways that ideas do not. Using complementary tools plus careful study and interpretation of the original text and figures, we were able to rework, yet only partially replicate, this experiment. Reading peer-reviewed manuscripts that cited Holmes’ 1934 report provided an additional level of insight into the interpretation and replication of this work in the decades that followed. From this, we touch on how experimental reworking can inform our strategies to address the reproducibility “crisis” in twenty-first century science.

High-throughput and accurate measurements of plant traits facilitate identification of gene function. Along with recent advances in quantitative genomics, there is a growing need for precise quantification of multiple traits in plants. However, it is difficult continuously to quantify plant adaptive responses to environmental stress responses such as drought because multiple environmental factors are intricately involved in the phenotype. To solve this problem, we developed an automatic phenotyping system for evaluating the growth responses of individual Arabidopsis plants to a wide range of environmental conditions. The RIKEN Integrated Plant Phenotyping System (RIPPS) controls soil moisture for single plants by automatically weighing and watering 120 continuously rotating pots under controlled light, humidity and temperature growth conditions. RIPPS also records individual rosette size and expansion rate by photographing plants every 2 h. We used RIPPS to establish phenotype evaluation methods for Arabidopsis growth response and water use efficiency under various water conditions, and analyzed the involvement of ABA metabolism in determining water use efficiency. We also used RIPPS to analyze salinity tolerance in Arabidopsis plants.

Comparison of day-neutral temperate maize and photoperiod-dependent teosinte revealed divergent leaf gene expression networks that implicate different genes of the same gene families in response to flowering., Temperate maize was domesticated from its tropical ancestor, teosinte. Whereas temperate maize is an autonomous day-neutral plant, teosinte is an obligate short-day plant that requires uninterrupted long nights to induce flowering. Leaf-derived florigenic signals trigger reproductive growth in both teosinte and temperate maize. To study the genetic mechanisms underlying floral inductive pathways in maize and teosinte, mRNA and small RNA genome-wide expression analyses were conducted on leaf tissue from plants that were induced or not induced to flower. Transcriptome profiles reveal common differentially expressed genes during floral induction, but a comparison of candidate flowering time genes indicates that photoperiod and autonomous pathways act independently. Expression differences in teosinte are consistent with the current paradigm for photoperiod-induced flowering, where changes in circadian clock output trigger florigen production. Conversely, differentially expressed genes in temperate maize link carbon partitioning and flowering, but also show altered expression of circadian clock genes that are distinct from those altered upon photoperiodic induction in teosinte. Altered miRNA399 levels in both teosinte and maize suggest a novel common connection between flowering and phosphorus perception. These findings provide insights into the molecular mechanisms underlying a strengthened autonomous pathway that enabled maize growth throughout temperate regions.

Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.

Key message Fusarium resistance in Arina is highly quantitative and governed by multiple small effect QTL. Anther retention has a high correlation with FHB susceptibility and appears a practicable indirect selection target for enhancing FHB resistance. Abstract The Swiss winter wheat cultivar Arina possesses a high resistance level constituted by a number of small to medium effect QTL reported from three independent mapping populations. Yet these overlap only for one resistance QTL on the long arm of chromosome 1B. The present study characterized Fusarium head blight (FHB) resistance in a population of 171 recombinant inbred lines from a cross between Arina (resistant) and Capo (moderately resistant). The population was evaluated for FHB resistance under field conditions for 3 years. Additionally, we phenotyped anther retention, plant height and flowering date to analyze their association with resistance. Lines with a low proportion of retained anthers after flowering and tall plants were significantly less diseased, while flowering date had no association with FHB severity. QTL analysis identified eight small to medium effect QTL for FHB severity, of which QTL on 1BS, 3B, 4AL and 6BL likely correspond to resistance alleles already detected in previously studied Arina populations. QTL for anther retention mapped to 4AL, 6BL and 5AS. Notably, QTL on 4AL and 6BL overlapped with QTL for FHB severity. A single small effect QTL for plant height was detected on 5AS and no QTL was identified for flowering date. Genotypes having three or four resistance alleles in combination showed a good resistance level, indicating pyramiding resistance QTL as a powerful approach for breeding resistant cultivars. Selection for rapid and complete anther extrusion appears promising as an indirect selection criterion for enhancing FHB resistance. Electronic supplementary material The online version of this article (doi:10.1007/s00122-015-2527-8) contains supplementary material, which is available to authorized users.

Genetic relationships between plant height and root morphology were investigated in a diverse set of wheat germplasm [199 double-haploid progeny derived from a cross between Avalon and Cadenza (Triticum aestivum L.), Rht near-isogenic lines (NILs), and accessions from the Watkins Collection] to investigate whether Rht genes controlling shoot height also control seedling root growth. A germination paper screen was developed to measure seedling root length (distinguishing seminal axes from seminal lateral roots), surface area, volume, and dry weight, and these were compared with shoot dry weight and the root to shoot ratio. Field experiments were conducted to measure mature plant height (PH) and grain characteristics for the mapping population. Forty-three quantitative trait loci (QTLs) for PH, root and seed traits were identified. Some QTLs for roots and either height or seed characteristics were coincident: chromosome 2D had co-locating root and PH QTLs; chromosomes 4D had co-locating root, PH, and seed QTLs; chromosome 5A and 6A had co-locating root and seed QTLs; and other non-co-locating root and PH QTLs were found on chromosomes 3A and 3B. Rht NILs illustrated that some known dwarfing genes reduce both PH and root proliferation. However, analysis of 25 short and 23 tall lines from the Watkins wheat germplasm collection indicated that PH and root proliferation are not simply related.

Fibre properties and the biochemical composition of cell walls are important traits in many applications. For example, the lengths of fibres define the strength and quality of paper, and lignin content is a critical parameter for the use of biomass in biofuel production. Identifying genes controlling these traits is comparatively difficult in woody species, because of long generation times and limited amenability to high-resolution genetic mapping. To address this problem, this study mapped quantitative trait loci (QTLs) defining fibre length and lignin content in the Arabidopsis recombinant inbred line population Col-4 × Ler-0. Adapting high-throughput phenotyping techniques for both traits for measurements in Arabidopsis inflorescence stems identified significant QTLs for fibre length on chromosomes 2 and 5, as well as one significant QTL affecting lignin content on chromosome 2. For fibre length, total variation within the population was 208% higher than between parental lines and the identified QTLs explained 50.58% of the observed variation. For lignin content, the values were 261 and 26.51%, respectively. Bioinformatics analysis of the associated intervals identified a number of candidate genes for fibre length and lignin content. This study demonstrates that molecular mapping of QTLs pertaining to wood and fibre properties is possible in Arabidopsis, which substantially broadens the use of Arabidopsis as a model species for the functional characterization of plant genes.

The C–S–A gene system determines rice hull pigmentation. A conserved color-producing model reveals the independent origin and evolution of the anthocyanin biosynthesis pathway in rice., Floral organs in rice (Oryza sativa) can be purple, brown, or red in color due to the accumulation of flavonoids, but the molecular mechanism underlying specific organ pigmentation is not clear. Here, we propose a C–S–A gene model for rice hull pigmentation and characterize it through genetic, molecular, and metabolomic approaches. Furthermore, we conducted phylogenetic studies to reveal the evolution of rice color. In this gene system, C1 encodes a R2R3-MYB transcription factor and acts as a color-producing gene, and S1 encodes a bHLH protein that functions in a tissue-specific manner. C1 interacts with S1 and activates expression of A1, which encodes a dihydroflavonol reductase. As a consequence, the hull is purple where functional A1 participation leads to high accumulation of cyanidin 3-O-glucoside. Loss of function of A1 leads to a brown hull color due to accumulation of flavonoids such as hesperetin 5-O-glucoside, rutin, and delphinidin 3-O-rutinoside. This shows a different evolutionary pathway of rice color in japonica and indica, supporting independent origin of cultivars in each subspecies. Our findings provide a complete perspective on the gene regulation network of rice color formation and supply the theoretical basis for extended application of this beneficial trait.

Highlight Drought-yield QTLs qDTY 2.2 and qDTY 4.1 improved rice variety IR64 complementarily through peak QTL effects at distinct stress levels, and by increasing root hydraulic conductance and root growth at depth., Characterizing the physiological mechanisms behind major-effect drought-yield quantitative trait loci (QTLs) can provide an understanding of the function of the QTLs—as well as plant responses to drought in general. In this study, we characterized rice (Oryza sativa L.) genotypes with QTLs derived from drought-tolerant traditional variety AdaySel that were introgressed into drought-susceptible high-yielding variety IR64, one of the most popular megavarieties in South Asian rainfed lowland systems. Of the different combinations of the four QTLs evaluated, genotypes with two QTLs (qDTY 2.2 + qDTY 4.1) showed the greatest degree of improvement under drought compared with IR64 in terms of yield, canopy temperature, and normalized difference vegetation index (NDVI). Furthermore, qDTY 2.2 and qDTY 4.1 showed a potential for complementarity in that they were each most effective under different severities of drought stress. Multiple drought-response mechanisms were observed to be conferred in the genotypes with the two-QTL combination: higher root hydraulic conductivity and in some cases greater root growth at depth. As evidenced by multiple leaf water status and plant growth indicators, these traits affected transpiration but not transpiration efficiency or harvest index. The results from this study highlight the complex interactions among major-effect drought-yield QTLs and the drought-response traits they confer, and the need to evaluate the optimal combinations of QTLs that complement each other when present in a common genetic background.

Differences between plant genomes range from single nucleotide polymorphisms to large-scale duplications, deletions and rearrangements. The large polymorphisms are termed structural variants (SVs). SVs have received significant attention in human genetics and were found to be responsible for various chronic diseases. However, little effort has been directed towards understanding the role of SVs in plants. Many recent advances in plant genetics have resulted from improvements in high-resolution technologies for measuring SVs, including microarray-based techniques, and more recently, high-throughput DNA sequencing. In this review we describe recent reports of SV in plants and describe the genomic technologies currently used to measure these SVs.

Key message Analysis of phenotypic data for 20 drought tolerance traits in 1–7 seasons at 1–5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04 has a high potential to enhance drought tolerance in chickpea improvement. Abstract Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50 % production losses in chickpea. In order to dissect the complex nature of drought tolerance and to use genomics tools for enhancing yield of chickpea under drought conditions, two mapping populations—ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261) segregating for drought tolerance-related root traits were phenotyped for a total of 20 drought component traits in 1–7 seasons at 1–5 locations in India. Individual genetic maps comprising 241 loci and 168 loci for ICCRIL03 and ICCRIL04, respectively, and a consensus genetic map comprising 352 loci were constructed (http://cmap.icrisat.ac.in/cmap/sm/cp/varshney/). Analysis of extensive genotypic and precise phenotypic data revealed 45 robust main-effect QTLs (M-QTLs) explaining up to 58.20 % phenotypic variation and 973 epistatic QTLs (E-QTLs) explaining up to 92.19 % phenotypic variation for several target traits. Nine QTL clusters containing QTLs for several drought tolerance traits have been identified that can be targeted for molecular breeding. Among these clusters, one cluster harboring 48 % robust M-QTLs for 12 traits and explaining about 58.20 % phenotypic variation present on CaLG04 has been referred as “QTL-hotspot”. This genomic region contains seven SSR markers (ICCM0249, NCPGR127, TAA170, NCPGR21, TR11, GA24 and STMS11). Introgression of this region into elite cultivars is expected to enhance drought tolerance in chickpea. Electronic supplementary material The online version of this article (doi:10.1007/s00122-013-2230-6) contains supplementary material, which is available to authorized users.

Key message Genetic control of maize grain carotenoid profiles is coordinated through several loci distributed throughout three secondary metabolic pathways, most of which exhibit additive, and more importantly, pleiotropic effects. Abstract The genetic basis for the variation in maize grain carotenoid concentrations was investigated in two F2:3 populations, DEexp × CI7 and A619 × SC55, derived from high total carotenoid and high β-carotene inbred lines. A comparison of grain carotenoid concentrations from population DEexp × CI7 grown in different environments revealed significantly higher concentrations and greater trait variation in samples harvested from a subtropical environment relative to those from a temperate environment. Genotype by environment interactions was significant for most carotenoid traits. Using phenotypic data in additive, environment-specific genetic models, quantitative trait loci (QTL) were identified for absolute and derived carotenoid traits in each population, including those specific to the isomerization of β-carotene. A multivariate approach for these correlated traits was taken, using carotenoid trait principal components (PCs) that jointly accounted for 97 % or more of trait variation. Component loadings for carotenoid PCs were interpreted in the context of known substrate-product relationships within the carotenoid pathway. Importantly, QTL for univariate and multivariate traits were found to cluster in close proximity to map locations of loci involved in methyl-erythritol, isoprenoid and carotenoid metabolism. Several of these genes, including lycopene epsilon cyclase, carotenoid cleavage dioxygenase1 and beta-carotene hydroxylase, were mapped in the segregating populations. These loci exhibited pleiotropic effects on α-branch carotenoids, total carotenoid profile and β-branch carotenoids, respectively. Our results confirm that several QTL are involved in the modification of carotenoid profiles, and suggest genetic targets that could be used for the improvement of total carotenoid and β-carotene in future breeding populations. Electronic supplementary material The online version of this article (doi:10.1007/s00122-013-2179-5) contains supplementary material, which is available to authorized users.