Causes and consequences of DNA content variation in Zea / Causas y consecuencias de la variación del contenido de ADN en Zea

ABSTRACT Cytogenetic evidence indicates that Zea, which comprises maize (Z. mays ssp. mays) and its wild relatives, is an allopolyploid genus. Our research group has carried out numerous cytogenetic studies on Zea species, mainly focused on native Argentinian and Bolivian maize landraces. We found a wide inter- and intraspecific genome size variation in the genus, with mean 2C-values ranging between 4.20 and 11.36 pg. For the maize landraces studied here, it varied between 4.20 and 6.75 pg. The objectives of this work are to analyze the causes of genome size variation and to discuss their adaptive value in Zea. This variation is mainly attributed to differences in the heterochromatin located in the knobs and to the amount of interspersed DNA from retrotransposons. Polymorphisms in presence or absence of B-chromosomes (Bs) and the population frequency of Bs are also a source of genome size variation, with doses ranging between one and eight in the landraces analyzed here. Correlation analysis revealed that the percentage of heterochromatin is positively correlated with genome size. In addition, populations cultivated at higher altitudes, which are known to be precocious, have smaller genome sizes than do those growing at lower altitudes. This information, together with the positive correlation observed between the length of the vegetative cycle and the percentage of heterochromatin, led us to propose that it has an adaptive role. On the other hand, the negative relationship found between Bs and heterochromatic knobs allowed us to propose the existence of an intragenomic conflict between these elements. We hypothesize that an optimal nucleotype may have resulted from such intranuclear conflict, where genome adjustments led to a suitable length of the vegetative cycle for maize landraces growing across altitudinal clines.

RESUMEN La evidencia citogenética indica que el género Zea, el maíz (Z. mays ssp. mays) y sus parientes silvestres, posee un origen alopoliploide. Nuestro grupo de investigación ha realizado numerosos estudios en especies de Zea, principalmente en maíces nativos de Argentina y Bolivia. En este género, hallamos una amplia variación inter e intraespecífica en el tamaño del genoma, con valores 2C medios que oscilan entre 4,20 y 11,36 pg. El valor 2C medio de los maíces nativos estudiados varió entre 4,20 y 6,75 pg. Los objetivos de este trabajo son analizar las causas de la variación del tamaño del genoma en Zea y discutir su valor adaptativo. Esta variación se atribuye principalmente a las diferencias en la heterocromatina de los knobs y en la cantidad de ADN intercalado de los retrotransposones. Otras fuentes de variación son los polimorfismos para presencia/ausencia de cromosomas B (Bs) y para la frecuencia poblacional de Bs en las razas analizadas, con dosis que oscilan entre uno y ocho Bs. El porcentaje de heterocromatina se correlaciona positivamente con el tamaño del genoma. Las poblaciones cultivadas en altitudes altas, que son precoces, tienen tamaños de genoma más pequeños que las que crecen en bajas altitudes. Esta información, junto con la correlación positiva observada entre la duración del ciclo vegetativo y el porcentaje de heterocromatina, nos llevó a proponer el rol adaptativo de la heterocromatina. Por otro lado, la relación negativa encontrada entre Bs y knobs heterocromáticos nos permitió proponer la existencia de un conflicto intragenómico entre estos elementos. Hipotetizamos que de este conflicto intranuclear habría resultado el nucleotipo óptimo, donde ajustes genómicos condujeron a una duración adecuada del ciclo vegetativo en las razas de maíz que crecen a lo largo de clines altitudinales.

Caracterización morfoestructural e índices zoométricos de hembras Ovino de Pelo Criollo Colombiano "OPC" Sudán

RESUMEN Objetivo. El objetivo de este estudio fue describir las medidas corporales e índices zoométricos de Ovinos de Pelo Criollos Colombianos (OPC), en dos de sus variedades, Sudán Bayo y Sudán Blanco. Materiales y métodos. Esta investigación fue llevada a cabo en los departamentos de Córdoba, Cesar y La Guajira, se visitaron dos granjas en cada uno de los primeros dos departamentos y una en el tercero. 21, 75 y 14 animales por departamento fueron evaluados, respectivamente. Se estudiaron 29 variables morfoestructurales y el peso corporal en 110 ovejas Sudán, y con estas variables evaluadas, se construyeron 15 índices zoométricos. A la información recolectada se le aplicó estadística descriptiva mediante el software InfoStat®. Resultados. Las Sudán Bayo presentaron valores superiores a las Sudán Blanco para el peso (40.8 y 40.57 kg), al igual que para todas las medidas zoométricas relativas a la cabeza, las extremidades y la mayoría de las del tronco; para la primera variedad se emplearon 83 ejemplares y para la segunda 27. En cuanto a los índices zoométricos, las Sudán se caracterizaron por ser dolicocraniotas, dolicocéfalas, eumétricas, de tórax con tendencia elíptica, de grupas convexilíneas y de acuerdo a dos índices etnológicos longilíneas, mientras que con base en un índice funcional brevilíneas. Conclusiones. A través de esta investigación se conoció de manera detallada el estado morfométrico actual de las OPC Sudán, así como también la proporcionalidad entre las regiones corporales de estas, cuya inclinación es hacia el biotipo cárnico. Esta información es de importancia para el conocimiento, caracterización racial, definición de biotipo, conservación, fomento y mejora genética de los OPC.

ABSTRACT Objective. The objective of this study was to describe the body measurements and zoometric indices of Sudán Bayo and Sudán Blanco, two breed varieties of Colombian creole woolless sheep (OPC). Materials and methods. This research was carried out in the departments of Córdoba, Cesar, and La Guajira. Two farms were visited in each of the first two departments and one farm in the third department. Twenty-one, 75, and 14 animals were evaluated in each department, respectively. Twenty-nine morphostructural variables and body weight were studied in 110 Sudán sheep. Based on this, 15 zoometric indices were also estimated. Descriptive statistic was applied to the information collected through the InfoStat® software. Results. Sudán Bayo sheep had higher values than Sudán Blanco sheep for the body weight (40.8 and 40.57 kg), as well as for all the zoometric measurements relative to the head and extremities, and most of the trunk morphometric measurements; in the first breed variety 83 ewes were used and in the second 27 individuals. Regarding the zoometric indices, Sudán sheep were characterized as dolichocranial, dolichocephalic, eumetric, of thorax with elliptical tendency, convex rump, and longilineal animals according to two ethnological indices while brevilineal animals based on one functional index. Conclusions. Through this investigation, the current morphometric status of Sudán OPC sheep was known in detail, as well as the proportionality between the corporal regions of these, whose inclination is towards the meat biotype. This information is of importance for the breed recognition and characterization, biotype definition, conservation, development, and genetic improvement of OPC sheep.

Caracterización morfológica y faneróptica de hembras Ovino de Pelo Criollo Colombiano "OPC" Sudán / Morphological and phaneroptic characterization of Sudan female Colombian Creole Hair Sheep "OPC"

RESUMEN Objetivo. Esta investigación tuvo como objetivo describir la morfología cualitativa y faneróptica de hembras Ovino de Pelo Criollo Colombiano (OPC) Sudán. Materiales y métodos. Se evaluaron seis características fanerópticas y siete morfológicas cualitativas en 115 hembras Sudán Bayo y Sudán Blanco, de los departamentos Córdoba, Cesar y La Guajira. Los datos obtenidos se analizaron a través del programa estadístico InfoStat® y se estimaron las frecuencias relativas y absolutas para cada uno de los caracteres evaluados. Resultados. Los OPC Sudán Bayo se distinguieron por ser de un color de capa bayo amarillo. Los Sudán Blanco fueron de capa overo castaño, pero predominando siempre el blanco sobre el castaño. Estos ovinos se caracterizaron por poseer mucosas negra-rosadas y en menor proporción habían individuos con mucosas rosadas. Además, presentaron orejas horizontales siempre, perfiles subconvexos en más del 80% de los casos, cuellos generalmente medianos y poco musculados, grupas usualmente inclinadas, ubres parcialmente pigmentadas y también despigmentadas. Asimismo, se caracterizaron por ostentar pezuñas veteadas mayoritariamente, aunque con un alto porcentaje de pezuñas claras en las Sudán Blanco. Conclusiones. Este trabajo ha permitido caracterizar de manera específica a las OPC Sudán desde la morfología y la faneróptica, obteniéndose así información de importancia para delimitar los parámetros de pertenencia a este grupo y para la propuesta de creación de un estándar racial.

ABSTRACT Objective. The objective of this research was to describe the qualitative morphology and phaneroptic of Sudán Colombian creole woolless sheep (OPC). Materials and methods. Six phaneroptic and seven qualitative morphological characteristics were evaluated in a total of 115 Sudán Bayo and Sudán Blanco ewes, from the departments Córdoba, Cesar and La Guajira. The data obtained were analyzed through the statistical program InfoStat®, relative and absolute frequencies were estimated for each evaluated trait. Results. Sudán Bayo OPC were distinguished by being yellow coat color. Sudán Blanco were white-and-chestnut spotted coat color, but white always predominated over chestnut. These ovines usually had black-rosy mucosae and in lesser amount there were individuals with rosy mucosae. Besides, they presented horizontal ears always, sub-convex profile in more than 80% of cases, generally medium-sized and scant muscled necks, usually inclined rumps, partially pigmented and depigmented udders as well. Likewise, they were characterized by showing marbled hooves mostly, but with a high percentage of clear hooves in Sudán Blanco sheep. Conclusions. This research has allowed to characterize specifically. Sudán OPC sheep from morphology and phaneroptic; thus, important information has been obtained to delimit the parameters of belonging to this group and for proposing the creation of a breed standard.

Temperature Effect on Traditional Pear (Pyrus communis L.) Landraces Seed Germination

Investigations included six traditional pear landraces (Pyrus communis L.): Aleksandra, Vodenka, Patlidjanka, Ljubichica, Tatlikuti and Crvenushka. The number of seeds per fruit, seed energy and total seed germination were investigated and statistically analysed (P = .05 and P = .01). Seed stratification encompassed pre-chilling by using three treatments: I treatment covers seed pre-chilling at -18°C for 24 hours; II treatment covers seed pre-chilling at +1°C for 2 weeks; III treatment covers seed pre-chilling at +8°C for 1 week. Only Patlidjanka belongs to the group with high seed number in the fruit. The other landraces produced low seed number like 2-3 seeds per fruit. The average number of all researched landraces is 3.67 seeds per fruit. The pear Tatlikuti showed a very high significant difference (P = .01). It was concluded that III treatment showed the highest seed energy at landraces Ljubichica 77.5% and Tatlikuti 75.0% and the lowest at Aleksandra 52.5%. There were significant differences (P = .05) between the applied treatments regarding seed energy. In II treatment, the total seed germination had the highest effect on Patlidjanka 87.75%. The values for germination seeds in the other landraces were in the range of 77.5% to 86.25%. Statistically, a significant difference was determined in the landraces Ljubichica and Crvenushka (P = .05), and there was high significant difference (P = .01) in the pear Aleksandra. The II and III treatments could be recommended as the most suitable to improve the pear seed germination.

Analysis of water soluble polysaccharides as a potential chemotaxonomic marker for landraces in Bixa orellana.

Annatto tree (Bixa orellana L.) is native to Brazil and is now under cultivation in many parts of world for its reddish orange ‘annatto’ dye. There are three types of landraces in annatto and they are distinguished based on fruit shape i.e., ovate, conical and hemispherical, whose pigment yield differs. Since annatto pigment yield varies with landrace, it is necessary to characterize markers towards the identification of landraces. In this study, we characterized water soluble polysaccharides (WSP) of twigs from three landraces using size-exclusion chromatography (SEC), fourier-transform Infrared spectroscopy (FT-IR), nuclear magnetic resonance spectroscopy (NMR) and gas liquid chromatography (GLC) for their potential use as chemotaxonomic markers to distinguish the landraces. GLC analysis on WSP showed hemispherical type contained 38% rhamnose, while conical and ovate types contained 17% and 34% glucose, respectively. Thus, glucose and rhamnose content of WSP could be used to distinguish the three landraces. Further, differences in calculated molecular weight as revealed by SEC (281.8, 151.3 and 79.4 kDa for conical, hemispherical and ovate types, respectively) could also be used to distinguish the three landraces.

Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers

Background: In order to evaluate the variation among different rice types, the genetic diversity in a rice collection composed by 59 breeding lines, 23 landraces, 18 weedy rice lines, and 35 introduced lines that collected from countries worldwide was analyzed using 134 simple sequence repeat markers. Results: In total, 1264 alleles were identified (average, 9.43 per locus). Rare alleles made up a large portion (58.4%) of the detected alleles, and 29 unique alleles associated with rice accessions were also discovered. A model-based structural analysis revealed the presence of three subpopulations. The genetic relationships revealed by the neighbour-joining tree method were fairly consistent with the structure-based membership assignments for most of the accessions. A total of 105 accessions (79.5%) showed a clear relationship to each cluster, while the remaining 27 accessions (20.5%) were categorized as admixtures. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide association mapping. The mean r² value for all intrachromosomal loci pairs was 0.1286. The LD between linked markers decreased with the genetic distance between pairs of linked loci. Conclusions: These results will provide an effective aid for future allele mining, association genetics, mapping and cloning gene(s), germplasm conservation, and improvement programs.

Characteristic differences in metabolite profile in male and female plants of dioecious Piper betle L.

Piper betle is a dioecious pan-Asiatic plant having cultural and medicinal uses. It belongs to the family Piperaceae and is a native of the tropics although it is also cultivated in subtropical areas. Flowering in P. betle occurs only in tropical regions. Due to lack of inductive floral cycles the plant remains in its vegetative state in the subtropics. Therefore, due to lack of flowering, gender distinction cannot be made the in the subtropics. Gender distinction in P. betle in vegetative state can be made using Direct Analysis in Real Time Mass Spectroscopy (DARTMS), a robust highthroughput method. DARTMS analysis of leaf samples of two male and six female plants showed characteristic differences in the spectra between male and female plants. Semi-quantitative differences in some of the identified peaks in male and female landraces showed gender-based differences in metabolites. Cluster analysis using the peaks at m/z 151, 193, 235 and 252 showed two distinct clusters of male and female landraces. It appears that male and female plants besides having flowers of different sexes also have characteristic differences in the metabolites representing two metabolic types.

Diversity in global maize germplasm: Characterization and utilization.

Maize (Zea mays L.) is not only of worldwide importance as a food, feed and as a source of diverse industrially important products, but is also a model genetic organism with immense genetic diversity. Although it was first domesticated in Mexico, maize landraces are widely found across the continents. Several studies in Mexico and other countries highlighted the genetic variability in the maize germplasm. Applications of molecular markers, particularly in the last two decades, have led to new insights into the patterns of genetic diversity in maize globally, including landraces as well as wild relatives (especially teosintes) in Latin America, helping in tracking the migration routes of maize from the centers of origin, and understanding the fate of genetic diversity during maize domestication. The genome sequencing of B73 (a highly popular US Corn Belt inbred) and Palomero (a popcorn landrace in Mexico) in the recent years are important landmarks in maize research, with significant implications to our understanding of the maize genome organization and evolution. Next-generation sequencing and high-throughput genotyping platforms promise to further revolutionize our understanding of genetic diversity and for designing strategies to utilize the genomic information for maize improvement. However, the major limiting factor to exploit the genetic diversity in crops like maize is no longer genotyping, but high-throughput and precision phenotyping. There is an urgent need to establish a global phenotyping network for comprehensive and efficient characterization of maize germplasm for an array of target traits, particularly for biotic and abiotic stress tolerance and nutritional quality. ‘Seeds of Discovery’ (SeeD), a novel initiative by CIMMYT with financial support from the Mexican Government for generating international public goods, has initiated intensive exploration of phenotypic and molecular diversity of maize germplasm conserved in the CIMMYT Gene Bank; this is expected to aid in effective identification and use of novel alleles and haplotypes for maize improvement. Multi-institutional efforts are required at the global level to systematically explore the maize germplasm to diversify the genetic base of elite breeding materials, create novel varieties and counter the effects of global climate changes.

Caracterização agronômica de populações locais de azevém na Região Sul do Brasil / Agronomic characterization of ryegrass landraces at Southern Brazil

Populações locais são fonte de variabilidade genética e adaptação para os programas de melhoramento; entretanto, pouco se sabe sobre as populações de azevém anual naturalizadas na América do Sul. Os objetivos deste trabalho foram analisar um conjunto de populações locais de azevém para produção de matéria seca e outros caracteres de importância agronômica e verificar a divergência existente entre essas populações. Foram avaliadas 36 populações, em um delineamento de blocos casualizados com quatro repetições. A produção de matéria seca variou de 1752,53 a 3905,67kg ha-1, com dezenove populações no grupo superior e a cultivar 'BRS Ponteio' como primeira do ranking. As populações brasileiras de azevém diferem para produção de matéria seca, bem como para produção de matéria seca no inverno e é possível identificar populações com ciclo produtivo mais longo.

Landraces are an important source of genetic variability in breeding programs. In spite of this, little is known about South American Italian ryegrass populations. The objectives of this research were to characterize a group of Brazilian Landraces of Italian ryegrass for dry matter production and other traits of agronomic importance, and to study genetic divergence among them. Thirty-seven populations were evaluated in a randomized block design with four replications. Dry matter production varied from 1752.53 to 3905.67kg ha-1, with nineteen populations in the most productive group and 'BRS Ponteio' ranking as the first one. Brazilian ryegrass populations differ for dry matter production and winter dry matter production. Populations with longer vegetative cycle may be identified.

Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces

Genetic diversity underlies the improvement of crops by plant breeding. Land races of rice (Oryza sativa L.) can contain some valuable alleles not common in modern germplasm. The aim here was to measure genetic diversity and its effect on agronomic traits among rice land-race genotypes grown in Pakistan. Diversity was measured using thirty-five microsatellite markers and seventy-five genotypes. Among the markers used a total of 142 alleles were detected at 32 polymorphic SSR loci, while three loci were monomorphic in Pakistani rice landraces. The number of alleles identified by each marker ranged from 2 to 13 with a mean of 4.4. Size differences between the smallest and largest alleles varied from 11bp to 71bp. Polymorphism information content ranged from 0.124 to 0.836, with an average of 0.569. At nine microsatellite loci, basmati-type landraces amplified more different alleles than those in the coarse-type. DNA markers RM70 and RM72 divided the rice landraces on the basis of days to flowering. A dendrogram based on total microsatellite polymorphism grouped 75 genotypes into four major clusters at 0.40 similarity coefficient, differentiating tall, late maturing and slender aromatic types from the short, early and bold non-aromatic ones. It inferred that Pakistani landraces have diverse genetic bases and can be utilized in future breeding programs. The DNA markers developed will assist in genotype identification, purity testing and plant variety protection.

Maize (Zea Mays L) landraces from the southern region of Brazil: contamination by Fusarium sp, zearalenone, physical and mechanical characteristics of the kernels

This work had as objectives the study of the physical and mechanical characteristics of maize kernels in relation to the contamination by Fusarium sp and by zearalenone in twenty landraces of maize from the southern region of Brazil. From the analyzed samples, 60 percent has been considered to have a hard endosperm type and 40 percent an intermediary one. A correlation between the physical and mechanical variables was observed as an indication that the higher is the proportion of hard endosperm, more dense will be the kernel and more force for its rupture will be necessary. The level of contamination by Fusarium sp was between 5.5 and 24.75 percent among the analyzed grains, correlating positively with the flotation index, indicating that the landraces of maize with a softer endosperm can present a higher contamination by this genus. The presence of zearalenone was verified in 75 percent of the samples, in concentrations varying from 50 to 640 µg kg-1.

Este trabalho teve por objetivos verificar as características físicas, mecânicas, contaminação por Fusarium sp e por zearalenona e suas relações, em vinte variedades crioulas de milho da região sul do Brasil. Verificou-se que das amostras analisadas, 60 por cento foram consideradas como possuidoras de endosperma do tipo duro e 40 por cento com endosperma do tipo intermediário. As variáveis físicas e mecânicas se correlacionaram, indicando que quanto maior a proporção de endosperma vítreo, mais denso e maior a força necessária até a ruptura do grão. A contaminação por Fusarium sp esteve entre 5,5 por cento e 24,75 por cento nos grãos analisados, correlacionando-se positivamente com o índice de flotação, indicando que as variedades crioulas de milho com uma maior proporção de endosperma macio podem apresentar uma maior contaminação por Fusarium sp, sugerindo-se a utilização de variedades crioulas com a textura do endosperma predominantemente vítrea. A presença de zearalenona foi verificada em 75 por cento das amostras, em concentrações que variaram de 50 a 640 µg kg-1.

Characterization of corn landraces planted grown in the campos gerais region (Paraná, Brazil) for industrial utilization

This work has the objective of characterizing twenty corn landraces grown in the Campos Gerais region (Paraná State) in relation to its chemical composition (moisture, ash, protein, ether extract, dietary fiber and starch) and physical properties (weight of 1000 grains, real density, flotation index, granulometry and color). In addition, also the lab scale processing of the kernels from the varieties was carried out for producing starch; starch purity was evaluated by measuring its protein contamination. Amylose contents and viscoamylograph profile were also evaluated. The results showed that the evaluated landraces have differences in chemical composition as well as in pericarp/endosperm/germ proportions and consequently it should have different industrial applications and interest for plant breeding.

Esse trabalho teve o objetivo de caracterizar vinte variedades de milho crioulo cultivadas na região dos Campos Gerais (Estado do Paraná) em relação a sua composição química (umidade, cinzas, proteína, extrato etéreo, fibra alimentar e amido) e propriedades físicas (peso de 1000 grãos, densidade real, índice de flotação, granulometria e cor) Além disso, foi feito o processamento dos grãos em escala de laboratório para a extração do amido, sendo mensurado o teor de proteína. Foram avaliados os conteúdos de amilose e o perfil viscoamilográfico. Os resultados mostraram que os milhos apresentaram diferentes composições químicas e proporções pericarpo/endosperma/ gérmen e consequentemente podem ter diferentes aplicações industriais e interesse ao melhoramento de plantas.

Development of a Brazilian maize core collection

The aim of this study was to evaluate methods for developing a Brazilian maize core collection. For an initial survey of the active collection, passport information, as well as characterization and evaluation of accessions, were taken into consideration, these then being divided according to geographic region and kernel-type. Multiple sampling methods were evaluated. The strategy of constant sampling generated extensive alterations in extract accession frequency. The multivariate strategy with dispersion graphs and principal components associated with the Tocher method was considered efficient for identifying the most divergent genotypes. The multivariate strategy generated greater alterations in the variance of traits. The average number of traits revealed few modifications with the various sampling strategies used. Therefore, the active collection could be considered as possessing a satisfactory amount of information for most of its accessions. Moreover, the multivariate strategy generated modifications in the variance of the traits, independent of sampling intensity.

Genetic diversity in Brazilian sweet potato (Ipomoea batatas (L.) Lam., Solanales, Convolvulaceae) landraces assessed with microsatellite markers

We used simple sequence repeat (SSR) markers to investigate the genetic diversity of 78 sweet potato (Ipomoea batatas) accessions (58 landraces and 20 putative clones) from traditional agricultural households from 19 local communities in the Vale do Ribeira, São Paulo, Brazil. Eight SSR loci were assessed using 6 percent (w/v) polyacrylamide gels stained with silver nitrate and the accessions genotyped considering the presence or absence of bands. The results were subjected to analysis of molecular variance (AMOVA), and cluster and principal coordinate analyses. Spatial structure was assessed using Mantel's test to compare genetic and geographic distances. Each primer pair generated between three and ten clearly scorable polymorphic fragments. Cluster analyses showed a Jaccard's index from 0.3 to 1.0, indicating high genetic and intravarietal diversity. Accessions from all 19 communities were not spatially structured (r = 0.15, p < 0.054), with AMOVA indicating that most of the variability (58.2 percent) was distributed within households and only 18.1 percent of the variability was distributed between households within communities. The outcrossing mating system of sweet potato, and anthropic factors such as selection of different varieties and their maintenance within household small plots and home gardens, as well as an extensive exchange system between agriculturists, may all be contributing to these results.