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Root colonizing Trichoderma fungi can stimulate plant immunity, but net effects are strain × cultivar-specific and changing ambient conditions further contribute to variable outcomes. Here, we used four Trichoderma spp. to inoculate seeds of four common bean (Phaseolus vulgaris) cultivars and explored in three different experimental setups the effects on fungal anthracnose after leaf inoculation with Colletotrichum lindemuthianum. Plants growing in pots with field soil under greenhouse conditions exhibited the highest and those in the open field the lowest overall levels of disease. Among 48 Trichoderma strain × bean cultivar × setup combinations, Trichoderma-inoculation enhanced disease in six and decreased disease in ten cases, but with the exception of T. asperellum B6-inoculated Negro San Luis beans, the strain × cultivar-specific effects on anthracnose severity differed among the setups, and anthracnose severity did not predict seed yield in the open field. In the case of Flor de Mayo beans, Trichoderma even reduced yield in anthracnose-free field plots, although this effect was counterbalanced in anthracnose-infected plots. We consider our work as a case study that calls for stronger emphasis on field experiments in the early phases of screenings of Trichoderma inoculants as plant biostimulants.

Quantification, using an accurate analytical approach, of capsinoids and capsaicinoids was performed on three chili pepper (Capsicum spp.) genotypes: “Chiltepı́n”, “Tampiqueño 74”, and “Bhut Jolokia” at various stages of fruit development. The accumulation of capsinoids, in all these peppers started between 10 to 20 days post-anthesis (dpa), increased and reached the highest capsinoid amount at 40 dpa, and then decreased until 60 dpa. Conversely, capsaicinoids could already be determined at 10 dpa in “Bhut Jolokia” and their accumulation pattern was different from that of the capsinoids in this genotype. The capsiate/dihydrocapsiate ratio presented a higher variation between genotypes and developmental stages than the capsaicin/dihydrocapsaicin ratio. Capsinoid ratios (4–24%) and Pun1/pAMT genotyping were determined. These results provide information on the progress of the accumulation of capsinoids in the aforementioned pungent and superhot cultivars and could support future breeding studies toward the understanding of the factors affecting their accumulation., This work forms part of the project RTA2015-00042-C02-01, funded by the National Institute for Agriculture and Food Research and Technology (INIA, Spain) and cofinanced by the European Fund for Regional Development (FEDER, Spain). It was also supported by A11-17R project and OT2017/032 (University of Cadiz, Spain).

Transcription factors are important regulators of gene expression. They can orchestrate the activation or repression of hundreds or thousands of genes and control diverse processes in a coordinated way. This work explores the effect of a master regulator of plant development, BOLITA (BOL), in plant metabolism, with a special focus on specialized metabolism. For this, we used an Arabidopsis thaliana line in which the transcription factor activity can be induced. Fingerprinting metabolomic analyses of whole plantlets were performed at different times after induction. After 96 h, all induced replicas clustered as a single group, in contrast with all controls which did not cluster. Metabolomic analyses of shoot and root tissues enabled the putative identification of differentially accumulated metabolites in each tissue. Finally, the analysis of global gene expression in induced vs. non-induced root samples, together with enrichment analyses, allowed the identification of enriched metabolic pathways among the differentially expressed genes and accumulated metabolites after the induction. We concluded that the induction of BOL activity can modify the Arabidopsis metabolome. Future work should investigate whether its action is direct or indirect, and the implications of the metabolic changes for development regulation and bioprospection.

Most of the commercial papaya genotypes show susceptibility to water deficit stress and require high volumes of irrigation water to yield properly. To tackle this problem, we have collected wild native genotypes of Carica papaya that have proved to show better physiological performance under water deficit stress than the commercial cultivar grown in Mexico. In the present study, plants from a wild Carica papaya genotype and a commercial genotype were subjected to water deficit stress (WDS), and their response was characterized in physiological and molecular terms. The physiological parameters measured (water potential, photosynthesis, Fv/Fm and electrolyte leakage) confirmed that the papaya wild genotype showed better physiological responses than the commercial one when exposed to WDS. Subsequently, RNA-Seq was performed for 4 cDNA libraries in both genotypes (susceptible and tolerant) under well-watered conditions, and when they were subjected to WDS for 14 days. Consistently, differential expression analysis revealed that after 14 days of WDS, the wild tolerant genotype had a higher number of up-regulated genes, and a higher number of transcription factors (TF) that were differentially expressed in response to WDS, than the commercial genotype. Thus, six TF genes (CpHSF, CpMYB, CpNAC, CpNFY-A, CpERF and CpWRKY) were selected for further qRT-PCR analysis as they were highly expressed in response to WDS in the wild papaya genotype. qRT-PCR results confirmed that the wild genotype had higher expression levels (REL) in all 6 TF genes than the commercial genotype. Our transcriptomic analysis should help to unravel candidate genes that may be useful in the development of new drought-tolerant cultivars of this important tropical crop.

As maize was domesticated in Mexico around 9,000 years ago, local farmers have selected and maintained seed stocks with particular traits and adapted to local conditions. In the present day, many of these landraces are still cultivated; however, increased urbanization and migration from rural areas implies a risk that this invaluable maize germplasm may be lost. In order to implement an efficient mechanism of conservation in situ, the diversity of these landrace populations must be estimated. Development of a method to select the minimum number of samples that would include the maximum number of alleles and identify germplasm harboring rare combinations of particular alleles will also safeguard the efficient ex‐situ conservation of this germplasm. To reach this goal, a strategy based on SSR analysis and a novel algorithm to define a minimum collection and rare genotypes using landrace populations from Puebla State, Mexico, was developed as a “proof of concept” for methodology that could be extended to all maize landrace populations in Mexico and eventually to other native crops. The SSR‐based strategy using bulked DNA samples allows rapid processing of large numbers of samples and can be set up in most laboratories equipped for basic molecular biology. Therefore, continuous monitoring of landrace populations locally could easily be carried out. This methodology can now be applied to support incentives for small farmers for the in situ conservation of these traditional cultivars.

Phaseolus vulgaris line A193 has been shown to be widely resistant to Colletotrichum lindemuthianum, including race 1472, one of the most virulent races of C. lindemuthianum characterized. Resistance to C. lindemuthianum race 1472 in P. vulgaris line A193 was investigated in segregating F2 and F2.3 populations from a cross between A193 and Flor de Mayo Bajio (a commercial cultivar highly susceptible to C. lindemuthianum). Resistance to 1472 in A193 was determined to be conditioned by a single dominant gene. Inoculation of crosses between A193 and cultivars Michigan Dark Red Kidney and Perry Marrow with race 1472 suggest that resistance in A193 is conditioned by the Co-1 gene. Inoculation of the cross A193 × Perry Marrow with C. lindemuthianum race 2, demonstrated that resistance to race 2 in Perry Marrow is also conditioned by a single dominant gene and is distinct to resistance in A193 or Michigan Dark Red Kidney. Three AFLP markers (ECAG/MACC-1, EACA/MAGA-2, EAGG/MAAC-8) linked in repulsion to the Co-1 locus were identified by screening the A193 × Flor de Mayo F2 population with 314 random amplified polymorphic DNA, amplified fragment length polymorphism, and restriction fragment length polymorphism markers. The two most closely linked markers should be useful in marker-assisted selection for Co-1.

Viroids are small, covalently closed, circular non-coding RNA pathogens of flowering plants. It is proposed that the symptoms of viroid pathogenesis result from a direct interaction between the viroid genomic RNA and unknown host plant factors. Using a comparative genomic approach we took advantage of the detailed annotation of the Arabidopsis thaliana (Arabidopsis) genome to identify sequence homologies between putative viroid-derived small RNAs (vd-sRNAs) and coding regions in the plant genome. A pool of sequence homologies among 29 species of the Pospiviroidae family and the Arabidopsis genome was analyzed. Using this strategy we identified putative host gene targets that may be involved in symptom expression in viroid-infected plants. In this communication, we report the in silico prediction and the experimental validation of pospiviroid-derived sRNAs conserved in the lower strand of the pathogenicity domain of seven viroid species infecting tomato; those vd-sRNAs targeted for cleavage the host mRNA encoding a conserved tomato WD40-repeat protein (SolWD40-repeat; SGN_U563134). Analysis of SolWD40-repeat expression indicated that this gene is down-regulated in tomato plants infected with tomato planta macho viroid (TPMVd). Furthermore, 5′ RLM-RACE revealed that the SolWD40-repeat mRNA is cleaved at the predicted target site showing complementarity to a corresponding TPMVd-sRNA identified in silico. Our approach proved to be useful for the identification of natural host genes containing sequence homologies with segments of the Pospiviroidae genome. Using this strategy we identified a functionally conserved gene in Arabidopsis and tomato, whose expression was modified during viroid infection in the host genome; regulation of this gene expression could be guided by vd-sRNA:mRNA complementarity, suggesting that the comparison of the Arabidopsis genome to viroid sequences could lead to the identification of unexpected interactions between viroid RNAs and their host.

The pathotypes of 17 isolates of Colletotrichum lindemuthianum from the central region of Mexico were characterized to determine the genetic relationship among isolates from this region and other regions of Mexico, and to evaluate the resistance present in the elite germ plasm collection of Phaseolus vulgaris at INIFAP. Eight pathotypes were identified, including pathotype 292, which is reported for the first time in Mexico. The lack of isolates infecting cultivar TU carrying the Co-5 resistance gene suggests that this cultivar is a useful source of resistance. Six pathotypes produced susceptible reactions on only differential cultivars of Middle American origin, one pathotype on a single cultivar of Andean origin, and one pathotype on cultivars of both Middle American and Andean origin. Comparison of amplified fragment length polymorphism (AFLP) genotypes of 21 isolates confirmed suggestions that populations of C. lindemuthianum are comprised of asexually reproducing clonal lineages. Analysis of five different pathotypes of C. lindemuthianum on 21 elite genotypes of P. vulgaris identified four genotypes from different races of P. vulgaris resistant to all five pathotypes. This information will allow breeders and farmers to select the resistant genotypes most suited to their needs.

The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies.

El mejoramiento del girasol (Helianthus annuus L.) depende en gran medida de la introducción de diversidad genética proveniente de material silvestre. El objetivo de este trabajo fue construir un mapa de ligamiento basado en marcadores AFLP a partir de una población F2:3 derivada de un cruzamiento inter-subespecífico de girasol (H. annuus var. macrocarpus x H. annuus ssp. texanus Heiser), así como detectar posiciones de loci de caracteres cuantitativos (QTL) a través del enfoque analítico de mapeo por intervalos. Se evaluaron los siguientes caracteres contrastantes entre girasoles cultivados y silvestres, presumiblemente relacionados con la domesticación: altura de planta, número de capítulos (ramificación) y diámetro de capítulos por planta, número y peso de aquenios por capítulo, días a floración, días a madurez fisiológica y contenido de aceite de aquenios. La evaluación fenotípica se llevó a cabo en condiciones de campo, con un diseño de bloques incompletos con dos repeticiones. Se consideró un nivel de significancia estadística de amplitud genómica de 0.05 en la detección de los QTL. Para establecer los valores críticos de los estadísticos de prueba se hicieron pruebas de permutación sólo con los grupos de ligamiento con puntuaciones LOD (logaritmo de la razón de verosimilitudes) > 1.5. Además, para cada carácter se hizo un análisis de varianza por locus individual no ligado, con lo cual se identificaron cuatro loci no ligados que afectan el número de aquenios por capítulo y los días a madurez fisiológica, con P < 0.001. Se identificó un QTL significativo con amplitud genómica de 0.017 para peso de aquenios que podría representar una región del genoma relacionada con la domesticación, y cinco QTLs posibles en cinco caracteres. Los QTLs detectados, que incluyen los hipotéticos, explicaron de 7.1 a 11.9 % de la varianza fenotípica.

Durante el 2003, se caracterizaron 13 variedades comerciales y tres líneas elite de papa mediante las técnicas de RAPD y SSR. Con la técnica de RAPD se evaluaron 40 iniciadores y se seleccionaron tres (Alpha ADN2, Alpha ADN23 y Alpha ADN30); Alpha ADN2 se usó individualmente, mientras que Alpha ADN23 y Alpha ADN30 se usaron de manera combinada. Con la técnica de SSR se evaluaron seis pares de iniciadores y se seleccionaron cuatro (M1F/M2R, M3F/M4R, M5F/M6R y M7F/M8R). Las relaciones genéticas entre genotipos se calcularon por el método de Similitud Genética. La matriz de distancias generada se utilizó para producir un dendrograma por medio de análisis de conglomerados (UPGMA). Todos los materiales fueron diferenciados por el patrón de fragmentos obtenidos con las dos técnicas utilizadas; con la técnica de RAPD se observaron un total de 26 fragmentos, de los cuales 69.23% fueron polimórfi cos y en SSR se obtuvieron un total de 49 fragmentos, de los cuales 83.67% fueron polimórfi cos. Se observó una gran similitud genética entre los materiales ya que la máxima distancia genética entre los diferentes grupos fue de 0.19. Las relaciones genéticas más cercanas fueron entre las variedades Sancal y NAU-6 con un valor de 88% en los intervalos de confi anza de Felsenstein. Se identifi caron ambos grupos de genotipos, unos * Recibido: Junio de 2005 Aceptado: Mayo de 2006 estrechamente relacionados y otros, como la variedad Monserrat, genéticamente distintos. Esta información permitirá diseñar los cruzamientos adecuados en el programa de mejoramiento.

AFLP was used to analyze the genetic diversity among Ochrobactrum strains. AFLP patterns showed a great genomic variability that separated the samples into three distinct clusters. Ochrobactrum intermedium was found to be closely related to Brucella abortus S99.

"Genetic relationships among isolates of Sclerotium cepivorum from different regions of Mexico, also one isolate from Spain and one from Venezuela were assessed based on the analysis of random amplified polymorphic DNAs (RAPDs). Five different oligonucleotide primers were used to detect genetic polymorphisms among 31 isolates from the three countries. Dendrogram indicated that the Mexican isolates formed two distinct groups, one consisted of the majority of isolates collected from a single field, and the other included isolates collected from different regions of Mexico and the Venezuelan isolate. The Spanish isolate occupied a unique terminal branch on the dendrogram, being the most divergent isolate in this analysis. These results suggest that considerable genetic diversity is present among different isolates of S. cepivorum in Mexico. "

"Pecina-Quintero, V., Martínez-de la Vega, O., Alvarado-Balleza,M. de J., Vandemark, G.J. y Williams-Alanís, H. 2001.Comparación de dos sistemas de marcadores moleculares enel análisis de las relaciones genéticas de Macrophomina phaseolina. Revista Mexicana de Fitopatología 19:128-139.Dos sistemas de marcadores moleculares (RAPDs y AFLPssimplificado), se compararon para evaluar su utilidad en la determinación de las relaciones genéticas de 21 aislados de Macrophomina phaseolina. Los dos sistemas fueron eficientes para discriminar entre los aislados de Arizona ydetectaron altos niveles de polimorfismos (RAPDs, 98.7% yAFLPs simplificado, 91.7%). Para cada sistema de marcador,se calcularon matrices de similaridad y matrices de distancia,con las que se generaron dendrogramas. Fue claro que losgrupos no están basados en el origen geográfico de las muestras. Las pruebas de correlación de producto momentode Pearson (P) y rangos de Spearman (S), sugieren una alta correlación entre ambos sistemas y métodos (P = 0.77% y S =0.90%), para estimar las relaciones genéticas. Asímismo, seobservó un alto índice de diversidad (0.84 y 0.71), proporciónmúltiple efectiva (12.66 y 17.5) e índice de marcador (10.65 y12.7) para RAPDs y AFLPs, respectivamente. Los resultadosse discuten en términos para la selección de la tecnología más apropiada, en la determinación de las relaciones genéticas."

A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078 ) have sequenced the Palomero Toluqueño ( Palomero ) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118 ) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115 ) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole ).

La soya [Glycine max (L.) Merrill] posee bajos niveles de diversidad genética en comparación con otras especies autógamas. Por lo anterior y con el fin de determinar si existe la necesidad de introducir nuevo germoplasma para generar nuevas variedades, se evaluó la diversidad genética de 24 líneas elite de soya para el trópico húmedo de México y nueve introducciones de otros países, mediante marcadores moleculares tipo AFLP. Los resultados revelaron que las líneas e introducciones no se agruparon de acuerdo a su origen geográfico, además de indicar un alto nivel de polimorfismos (60 %). Los genotipos de México son altamente similares a los de Brasil. El índice dediversidad genética fue bajo (31 %), y semejante a los reportados en otros estudios con RFLP y RAPD. Aunque la muestra de genotipos no representó a la totalidad del germoplasma de soya cultivada en el trópico húmedo de México, se considera que existe suficiente diversidad genética para generar nuevas variedades, ya que tres líneas mexicanas fueron más divergentes a nivel molecular que los materiales considerados filogenéticamente distintos de otros países (basados en características morfológicas y fisiológicas) utilizados como testigos.