Genomic Prediction of Resistance to Tan Spot, Spot Blotch and Septoria Nodorum Blotch in Synthetic Hexaploid Wheat.

Genomic prediction combines molecular and phenotypic data in a training population to predict the breeding values of individuals that have only been genotyped. The use of genomic information in breeding programs helps to increase the frequency of favorable alleles in the populations of interest. This study evaluated the performance of BLUP (Best Linear Unbiased Prediction) in predicting resistance to tan spot, spot blotch and Septoria nodorum blotch in synthetic hexaploid wheat. BLUP was implemented in single-trait and multi-trait models with three variations: (1) the pedigree relationship matrix (A-BLUP), (2) the genomic relationship matrix (G-BLUP), and (3) a combination of the two matrices (A+G BLUP). In all three diseases, the A-BLUP model had a lower performance, and the G-BLUP and A+G BLUP were statistically similar (p ≥ 0.05). The prediction accuracy with the single trait was statistically similar (p ≥ 0.05) to the multi-trait accuracy, possibly due to the low correlation of severity between the diseases.

Genomic Prediction from Multi-Environment Trials of Wheat Breeding.

Genomic prediction relates a set of markers to variability in observed phenotypes of cultivars and allows for the prediction of phenotypes or breeding values of genotypes on unobserved individuals. Most genomic prediction approaches predict breeding values based solely on additive effects. However, the economic value of wheat lines is not only influenced by their additive component but also encompasses a non-additive part (e.g., additive × additive epistasis interaction). In this study, genomic prediction models were implemented in three target populations of environments (TPE) in South Asia. Four models that incorporate genotype × environment interaction (G × E) and genotype × genotype (GG) were tested: Factor Analytic (FA), FA with genomic relationship matrix (FA + G), FA with epistatic relationship matrix (FA + GG), and FA with both genomic and epistatic relationship matrices (FA + G + GG). Results show that the FA + G and FA + G + GG models displayed the best and a similar performance across all tests, leading us to infer that the FA + G model effectively captures certain epistatic effects. The wheat lines tested in sites in different TPE were predicted with different precisions depending on the cross-validation employed. In general, the best prediction accuracy was obtained when some lines were observed in some sites of particular TPEs and the worse genomic prediction was observed when wheat lines were never observed in any site of one TPE.

A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.).

BACKGROUND: Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. RESULTS: A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. CONCLUSION: We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications.

Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris.

BACKGROUND: The development of genetic markers is complex and costly in species with little pre-existing genomic information. Faba bean possesses one of the largest and least studied genomes among cultivated crop plants and no gene-based genetic maps exist. Gene-based orthologous markers allow chromosomal regions and levels of synteny to be characterised between species, reveal phylogenetic relationships and chromosomal evolution, and enable targeted identification of markers for crop breeding. In this study orthologous codominant cross-species markers have been deployed to produce the first exclusively gene-based genetic linkage map of faba bean (Vicia faba), using an F6 population developed from a cross between the lines Vf6 (equina type) and Vf27 (paucijuga type). RESULTS: Of 796 intron-targeted amplified polymorphic (ITAP) markers screened, 151 markers could be used to construct a comparative genetic map. Linkage analysis revealed seven major and five small linkage groups (LGs), one pair and 12 unlinked markers. Each LG was comprised of three to 30 markers and varied in length from 23.6 cM to 324.8 cM. The map spanned a total length of 1685.8 cM. A simple and direct macrosyntenic relationship between faba bean and Medicago truncatula was evident, while faba bean and lentil shared a common rearrangement relative to M. truncatula. One hundred and four of the 127 mapped markers in the 12 LGs, which were previously assigned to M. truncatula genetic and physical maps, were found in regions syntenic between the faba bean and M. truncatula genomes. However chromosomal rearrangements were observed that could explain the difference in chromosome numbers between these three legume species. These rearrangements suggested high conservation of M. truncatula chromosomes 1, 5 and 8; moderate conservation of chromosomes 2, 3, 4 and 7 and no conservation with M. truncatula chromosome 6. Multiple PCR amplicons and comparative mapping were suggestive of small-scale duplication events in faba bean. This study also provides a preliminary indication for finer scale macrosynteny between M. truncatula, lentil and faba bean. Markers originally designed from genes on the same M. truncatula BACs were found to be grouped together in corresponding syntenic areas in lentil and faba bean. CONCLUSION: Despite the large size of the faba bean genome, comparative mapping did not reveal evidence for polyploidisation, segmental duplication, or significant rearrangements compared to M. truncatula, although a bias in the use of single locus markers may have limited the detection of duplications. Non-coding repetitive DNA or transposable element content provides a possible explanation for the difference in genome sizes. Similar patterns of rearrangements in faba bean and lentil compared to M. truncatula support phylogenetic studies dividing these species into the tribes Viceae and Trifoliae. However, substantial macrosynteny was apparent between faba bean and M. truncatula, with the exception of chromosome 6 where no orthologous markers were found, confirming previous investigations suggesting chromosome 6 is atypical. The composite map, anchored with orthologous markers mapped in M. truncatula, provides a central reference map for future use of genomic and genetic information in faba bean genetic analysis and breeding.

Seed and seedling quality of three chilis (Capsicum annuum L.) native to Oaxaca, Mexico / Qualidade de sementes e plântulas de três pimentas (Capsicum annuum L.) endêmicas de Oaxaca, México

ABSTRACT: The diversity of chilis in Oaxaca is one of the most extensive in Mexico. Growers select seeds in the traditional manner; information on its quality is unknown. The aim of this research was to compare the physical and physiological quality of seeds and seedlings of three native types to chili (Huacle, De agua and Pasilla) and of the commercial Green pepper as control. Fifteen variables were evaluated in seed and twelve in seedlings. The laboratory experiments were established under a completely randomized design. Means of the variables were compared using the Tukey test (α=0.05). Results showed that Pasilla chili had the highest values in seed size and weight, which was 1.44 g heavier than the control and 2.09 to 3.73 g higher than native types. Haucle chili and green pepper had a 90% germination rate, while chili De agua and Pasilla chili had germination rates of 51 and 38%, respectively. Huacle chili had the highest germination rate index (29.89) and seedling vigor index (992.25). The top highest values of number of normal seedlings were obtained in the control and Huacle chili seedlings (72 and 88%); also, the latter had the longest plumule (3.36 cm) and radicle (7.67 cm) values. Both Huacle and Pasilla chili seedlings had larger values in height, stem thickness, number of leaves, leaf area and slenderness index than De agua and Green pepper. Huacle chili had good physical and physiological quality similar to the seeds of the commercial Green pepper.

RESUMO: Oaxaca é umas das regiões de maior diversidade de espécies de pimentas do México. Os agricultores selecionam sementes da maneira tradicional; informações sobre sua qualidade são desconhecidas. O objetivo desta pesquisa foi comparar a qualidade física e fisiológica de sementes e mudas de três tipos nativos de pimenta (Huacle, De Agua e Pasilla) e pimenta verde comercial como controle. Quinze variáveis foram avaliadas em sementes e doze em mudas. As experiências de laboratório foram estabelecidas sob um delineamento inteiramente casualizado. As médias das variáveis foram comparadas pelo teste de Tukey (α=0.05). Os resultados mostraram que o Pasilla apresentou os maiores valores em tamanho e peso de sementes, 1,44 g mais pesado que o controle e 2,09 a 3,73 g maior que os demais tipos de pimenta nativa. A pimenta Huacle e a pimenta verde tiveram 90% de germinação de 90%, enquanto que De Agua e Pasilla foi de 51 e 38%, respectivamente. A pimienta Huacle apresentou os maiores índices de taxa de germinação (29,89) e de vigor de plântulas (992,25). Os maiores valores máximos no número de mudas normais foram obtidos no controle e na pimenta Huacle (72 e 88%). Além disso, este último apresentou os maiores valores de plúmula (3,36 cm) e radícula (7,67 cm). As mudas do Huacle e Pasilla apresentaram maiores valores em altura, espessura do caule, número de folhas, área foliar e índice de esbelto em relação à pimenta, De agua e ao controle. O Huacle apresentou boa qualidade física e fisiológica, semelhante às sementes da pimentão comercial.