M. Isabel Vales

Single Nucleotide Polymorphism Genotyping for Breeding and Genetics Applications in Chickpea and Pigeonpea using the BeadXpress Platform

Single nucleotide polymorphisms (SNPs) are ideal molecular markers due to their higher abundance. Although several types of genotyping platforms for assaying large number of SNPs are available, in cases such as marker‐assisted selection, where few markers are required for genotyping a set of potential lines, high‐throughput SNP genotyping platforms (e.g., iScan or Infinium) may not be cost effective. In this scenario, GoldenGate assays based on VeraCode technology using Illumina BeadXpress seems to be the most cost‐effective platform. The objective of this study was to develop cost‐effective SNP genotyping platforms in chickpea (Cicer arietinum L.) and pigeonpea (Cajanus cajan L.). Two sets of SNPs, one each for chickpea (96 SNPs) and pigeonpea (48 SNPs), were developed and tested by genotyping 288 diverse genotypes from respective reference sets. The SNPs selected for the oligo pool assays had high transferability to crop wild relative species. The mean polymorphism information content value of assayed SNP markers was 0.31 and 0.32 in chickpea and pigeonpea, respectively. No unique pattern was observed in the chickpea reference set whereas two major groups were observed in the case of the pigeonpea reference set. The Illumina BeadXpress platform assays developed for chickpea and pigeonpea are highly informative and cost effective for undertaking genetic studies in these legume species.

Map-based analysis of genetic loci on chromosome 2D that affect glume tenacity and threshability, components of the free-threshing habit in common wheat (Triticum aestivum L.).

During the domestication of bread wheat (Triticum aestivum L.), evolutionary modifications that took place in seed dispersal mechanisms enhanced its suitability for agricultural production. One of these modifications involved the evolution of the free-threshing or hulless characteristic. In this study, we studied quantitative trait loci (QTL) affecting components of the free-threshing habit (threshability and glume tenacity) on chromosome 2D in a recombinant inbred line (RIL) population developed by the International Triticeae Mapping Initiative (ITMI) as well as the tenacious glumes 1 (Tg1) gene in F2 progeny (CS/CS2D F2) of a cross between Chinese Spring and the 2D2 substitution line [Chinese Spring (Ae.tauschii 2D)]. In the ITMI population, two QTL affected threshability (QFt.orst-2D.1 and QFt.orst-2D.2) and their location coincided with QTL affecting glume tenacity (QGt.orst-2D.1 and QGt.orst-2D.2). In the CS/CS2D F2 population, the location of QTL that affected glume tenacity (QGt.orst-2D.1), the size of a glume base scar after detachment (QGba.orst-2D), and Tg1 (12-cM interval between Xwmc112 and Xbarc168) also coincided. Map comparisons suggest that QFt-orst-2D.1, QGt.orst-2D.1, and QGba.orst-2D correspond to Tg1 whereas QFt.orst-2D.2 and QGt.orst-2D.2 appear to represent separate loci. The observation of coincident QTL for threshability and glume tenacity suggests that threshability is a function of glume adherence. In addition, the observation of the coincident locations of Tg1 and QTL for the force required to detach a glume and the size of a glume base scar after detachment suggests that Tg1’s effect on both glume tenacity and threshability resides on its ability to alter the level of physical attachment of glumes to the rachilla of a spikelet.

RMo1 Confers Blast Resistance in Barley and Is Located within the Complex of Resistance Genes Containing Mla, a Powdery Mildew Resistance Gene

Isolates of Magnaporthe oryzae (the causal agent of rice blast disease) can infect a range of grass species, including barley. We report that barley Hordeum vulgare cv. Baronesse and an experimental line, BCD47, show a range of resistance reactions to infection with two rice blast isolates. The complete resistance of Baronesse to the isolate Ken 54-20 is controlled by a single dominant gene, designated RMo1. RMo1 mapped to the same linkage map position on chromosome 1H as the powdery mildew resistance locus Mla and an expressed sequence tag (k04320) that corresponds to the barley gene 711N16.16. A resistance quantitative trait locus (QTL), at which Baronesse contributed the resistance allele, to the isolate Ken 53-33 also mapped at the same position as RMo1. Synteny analysis revealed that a corresponding region on rice chromosome 5 includes the bacterial blight resistance gene xa5. These results indicate that a defined region on the short arm of barley chromosome 1H, including RMo1 and Mla, harbors genes conferring qualitative and quantitative resistance to multiple pathogens. The partial resistance of BCD47 to Ken53-33 is determined by alleles at three QTL, two of which coincide with the linkage map positions of the mildew resistance genes mlo and Mlf.

Chloroplast and nuclear microsatellite analysis of Aegilops cylindrica.

Aegilops cylindrica Host (2n=4x=28, genome CCDD) is an allotetraploid formed by hybridization between the diploid species Ae. tauschii Coss. (2n=2x=14, genome DD) and Ae. markgrafii (Greuter) Hammer (2n=2x=14, genome CC). Previous research has shown that Ae. tauschii contributed its cytoplasm to Ae. cylindrica. However, our analysis with chloroplast microsatellite markers showed that 1 of the 36 Ae. cylindrica accessions studied, TK 116 (PI 486249), had a plastome derived from Ae. markgrafii rather than Ae. tauschii. Thus, Ae. markgrafii has also contributed its cytoplasm to Ae. cylindrica. Our analysis of chloroplast and nuclear microsatellite markers also suggests that D-type plastome and the D genome in Ae. cylindrica were closely related to, and were probably derived from, the tauschii gene pool of Ae. tauschii. A determination of the likely source of the C genome and the C-type plastome in Ae. cylindrica was not possible.

Hybridization between wheat and jointed goatgrass (Aegilops cylindrica) under field conditions

Abstract Jointed goatgrass is an important weed of wheat in the United States and other parts of the world. Under field conditions, wheat and jointed goatgrass can hybridize and produce backcross derivatives, a situation that may allow gene flow between these two species. In order to gain a better understanding of the factors governing gene flow, a study to characterize patterns of mating between these two species was undertaken. Chloroplast and nuclear microsatellite markers were used to evaluate the parentage of 413 first-generation backcross (BC1) seeds obtained from 127 wheat–jointed goatgrass F1 hybrids, produced naturally under field conditions. Of the 127 hybrids evaluated, 109 (85.8%) had jointed goatgrass as the female parent, whereas the remaining 18 F1 plants (14.2%) had wheat as the female parent. Of the 413 BC1 plants analyzed, 358 (86.7%) had wheat and 24 (5.8%) had jointed goatgrass as the male backcross parent. The male parentage of 31 BC1 (7.5%) plants could not be determined. Under natural field conditions, wheat was the prevalent pollen donor for the production of hybrids and first-generation backcross derivatives. However, hybrids and backcrosses with jointed goatgrass as the male parent also were observed. Thus, the establishment and persistence of a zone of hybridization between these species would result in the development of jointed goatgrass carrying wheat genes. Nomenclature: Jointed goatgrass, Aegilops cylindrica Host AEGCY; wheat, Triticum aestivum L.

Resistance of potato germplasm to the potato tuberworm (Lepidoptera: Gelechiidae).

ABSTRACT The evaluation of potato germplasm for resistance to potato tuberworm, Phthorimaea operculella (Zeller) (Lepidoptera: Gelechiidae), is a valuable component of integrated pest management; however, few attempts have been made to identify natural genetic tuber resistance to tuberworm on potato germplasm. The objective of this study was to screen potato germplasm with potential tuberworm resistance for tuber resistance under field and laboratory conditions. Experiments were conducted over a 2-yr period at the Hermiston Agricultural Research and Extension Center, Hermiston, OR. Of 125 germplasm that were tested in 2006, q13 were selected for further screening in 2007. These germplasm were: A0008-1TE, A97066LB, NY123, PA00N10-5, PA99N2, PA99N82, Paciencia, Q174-2, Russet Burbank, Rubi, Ranger Russet, Spunta G2, and T88-4. Tuber resistance of potato germplasm was determined based on the number of mines per tuber and the number of live larvae. Tubers of transgenic clone Spunta G2 were resistant to tuberworm damage. All other germplasm tested in this study, including Russet Burbank and Ranger Russet, were susceptible to tuberworm in the field and laboratory experiments. Incorporation of host plant resistance to tuber penetration by larvae together with appropriate cultural practices including limiting exposure time of tubers in the field may provide the best management option in the future.

Maize Centromere Mapping: A Comparison of Physical and Genetic Strategies

Centromere positions on 7 maize chromosomes were compared on the basis of data from 4 to 6 mapping techniques per chromosome. Centromere positions were first located relative to molecular markers by means of radiation hybrid lines and centric fission lines recovered from oat-maize chromosome addition lines. These centromere positions were then compared with new data from centric fission lines recovered from maize plants, half-tetrad mapping, and fluorescence in situ hybridizations and to data from earlier studies. Surprisingly, the choice of mapping technique was not the critical determining factor. Instead, on 4 chromosomes, results from all techniques were consistent with a single centromere position. On chromosomes 1, 3, and 6, centromere positions were not consistent even in studies using the same technique. The conflicting centromere map positions on chromosomes 1, 3, and 6 could be explained by pericentric inversions or alternative centromere positions on these chromosomes.

Molecular Analysis of Potatoes from the Pacific Northwest Tri-State Variety Development Program and Selection of Markers for Practical DNA Fingerprinting Applications

DNA fingerprinting is a valuable tool for plant cultivar discrimination and identification. Simple Sequence Repeat (SSR) markers represent an excellent option for obtaining DNA fingerprints of potatoes in an easy, fast, and reliable fashion. The highly polymorphic and co-dominant nature of SSRs gives them good discrimination power to declare the distinctiveness of new potato clones for Plant Variety Protection (PVP) and to properly identify existing cultivars. They are also useful for confirming origin and avoiding duplications and mixtures in breeding, foundation and certification programs, and also during growing and marketing stages. A total of 54 (50 tetraploid and 4 diploid) potato clones, including new cultivars released by the Pacific Northwest Tri-State Potato Variety Development Program and a set of common commercial cultivars, were analyzed using 25 SSR markers. Marketing classes (French fry processing, fresh market, and chip processing) were clearly separated using those markers. We have empirically selected a subset of six SSRs that differentiate all the potato varieties and clones present in the study. This subset of six SSR markers could be used for practical DNA fingerprinting. In order to declare distinctiveness, we recommend that common reference varieties always be genotyped together with the newly tested potato clones and that focus be placed on the relative allelic differences between the new clones and the reference varieties.ResumenLa huella genética es una valiosa herramienta para identificar y diferenciar cultivares vegetales. Los marcadores basados en repeticiones de secuencias simples (SSR) son una excelente opción para obtener huellas genéticas en papas de una manera fácil, rápida y eficaz. La naturaleza co-dominante y el alto polimorfismo de los marcadores SSR permiten tener un alto poder discriminatorio para declarar la singularidad de los nuevos clones de papa para la Protección de Variedades Vegetales (PVP) e identificación de cultivares existentes. Son también útiles para confirmar el origen de los cultivares y evitar así duplicidades y mezclas en los programas de mejoramiento, fundación y certificación así como en las etapas posteriores de cultivo y comercialización. Un total de 54 clones de papa (cincuenta tetraploides y cuatro diploides), incluyendo los cultivares más recientes desarrollados por el Programa Tri-estatal de Desarrollo de Variedades de Papa de la Región del Pacífico Noroccidental y un conjunto de cultivares comerciales de uso común, fueron analizados usando 25 marcadores SSR. Usando estos marcadores, los cultivares fueron claramente diferenciados según su uso final (procesamiento para papas fritas, papa tipo chip y uso en fresco). Empíricamente se seleccionó un grupo de seis marcadores SSR que diferencian los 54 clones y variedades presentes en este estudio. Este subconjunto de seis marcadores podría usarse en la práctica para determinar la huella genética. Para declarar la singularidad de variedades y clones recomendamos incluir variedades conocidas de referencia en el proceso de genotipado junto con los clones nuevos que van a evaluarse con especial énfasis en las diferencias relativas de los alelos presentes entre las variedades de referencia y los nuevos clones.

Yukon Gem: A Yellow-Fleshed Potato Cultivar Suitable for Fresh-Pack and Processing with Resistances to PVYO and Late Blight

Yukon Gem is a yellow-fleshed, medium to early-maturing cultivar suitable for fresh-pack or processing with a high level of resistance to potato virus YO, and moderate foliar and tuber resistance to late blight. Multiple trials demonstrated a higher yield potential than Yukon Gold (yellow-fleshed industry standard). Yukon Gem produces uniform attractive tubers with light yellow skin and splashes of pink around the eyes; with flesh color similar to Yukon Gold. Yukon Gem was obtained from the intercrossing of Brodick and Yukon Gold at North Dakota State University (NDSU). An NDSU seedling tuber was sent and selected at Aberdeen, ID in 1995 and designated NDA5507-3YF. It advanced through the Aberdeen potato breeding program and regional trials in the western and northwestern U.S. Yukon Gem was released in 2006 by the USDA-ARS and the Agricultural Experiment Stations of Idaho, Oregon, and Washington, and is a product of the Northwest Potato Variety (Tri-State) Development Program.ResumenYukon Gem es una variedad de pulpa amarilla, de ciclo medio a temprano, ideal para empaque fresco o para proceso con un alto nivel de resistencia al virus YO, con moderada resistencia del follaje y del tubérculo al tizón tardío. Se ha demostrado en múltiples ensayos un potencial de rendimiento más alto que Yukon Gold (pulpa amarilla, estándar para la industria). Yukon Gem produce tubérculos uniformes atractivos con piel ligeramente amarilla y algo de rosado alrededor de los ojos; con color de pulpa similar al de Yukon Gold. Yukon Gem se obtuvo del entrecruzamiento de Brodick y Yukon Gold en la Universidad Estatal de Dakota del Norte (NDSU). Se envió un minitubérculo de NDSU y se seleccionó en Aberdeen, ID en 1995, designándosele NDA5507-3YF. Avanzó a lo largo del programa de mejoramiento de papa de Aberdeen y en las pruebas regionales en el oeste y noroeste de EUA. Yukon Gem se liberó en el 2006 por el USDA-ARS y por las Estaciones Agrícolas Experimentales de Idaho, Oregon, y Washington, y es un producto del Programa de Desarrollo de Variedades de Papa del Noroeste (Tri-State).

Multiple-site identification of potato parent clones conferring high levels of late blight resistance with a corresponding genetic model for resistance

Toluca Valley, Mexico, is the putative center of origin and diversity forPhytophthora infestans (Mont.) de Bary, the oomycete pathogen responsible for late blight, making it an ideal location for screening potato breeding populations for late blight resistance. Approximately 21,500 progeny from the USDA-ARS, Aberdeen, Idaho potato breeding program were evaluated from 1996 through 2005 by estimating the percentage of defoliation due to late blight throughout the growing season. Comparisons of the number of resistant progeny and their degree of resistance response from resistant x susceptible (RxS) and resistant x resistant (RxR) crosses were made across years. A clone of each progeny planted in Toluca Valley was also planted the same year near Aberdeen, Idaho, to screen for acceptable tuber type. Promising progeny phenotypes were then screened the following year for tuber late blight resistance at field plots near Corvallis, Oregon. The RxR late blight crosses produced 64% resistant progeny compared to 29% of the RxS crosses. The segregation for late blight resistance in progeny from specific RxS crosses best fits a 1R:3S ratio. This segregation ratio is best explained by a gene model in which resistance is conferred by the presence of a dominant allele at each of two loci. The greater percentage of resistant progeny from RxR crosses indicates the benefits of pyramiding resistance genes from diverse germplasm. Three promising late blight resistant parental clones with acceptable tuber type resulted from family A95053. Family A95053 has multiple sources of resistance that includeSolarium demissum andSolarium stoloniferum, via female parent AWN86514-2 and male parent, B0718-3.ResumenEl valle de Toluca, México, es el supuesto centro de origen y diversidad dePhytophthora infestans (Mont.) de Bary, el Oomycete responsable del tizón tardío, lo cual hace que sea el lugar ideal para el tamizado de poblaciones resistentes. Aproximadamente 21,500 progenies del Programa de mejoramiento del USDA-ARS, Aberdeen, Idaho, fueron evaluadas desde 1996 hasta el 2005 inclusive, estimando el porcentaje de defoliación debido a tizón tardío durante toda la campaña agrícola. Se hicieron a través de los años comparaciones del número de progenies resistentes y el grado de respuesta de los cruzamientos resistente x susceptible (R x S) y resistente x resistente (R x R). Un clon de cada progenie sembrado en el valle de Toluca se sembró el mismo año cerca de Aberdeen, Idaho, para tamizar el tipo aceptable de tubérculo. Los fenotipos de la progenie promisoria fueron luego tamizados el siguiente año para resistencia al tizón tardío en parcelas cerca de Corvallis, Oregon. Los cruzamiento R x R produjeron 64% de progenie resistente, en comparación con el 29% de cruzamientos R x S. La segregación para resistencia al tizón tardío en la progenie R x S concuerdan con la proporción 1R:3S. Esta proporción de segregación está mejor explicado por un modelo genético, en el cual la resistencia está conferida por la presencia de un alelo dominante en cada uno de dos loci. El mayor porcentaje de progenie resistente de cruzamientos R x R indica los beneficios de acumular en pirámide genes de resistencia de germoplasma diverso. Tres clones promisorios progenitores de resistencia a tizón tardío con tipo de tubérculo aceptable resultaron de la familia A95053. La familia A95053 tiene fuentes múltiples de resistencia que incluyenSolanum demissum ySolanum stoloniferum vía progenitor femenino AWN86514-2 y progenitor masculino B0718-3.