James S. Beaver

Improving efficiency of breeding for higher crop yield

SummaryExclusive selection for yield raises, the harvest index of self-pollinated crops with little or no gain in total bipmass. In addition to selection for yield, it is suggested that efficient breeding for higher yield requires simultaneous selection for yields three major, genetically controlled physiological components. The following are needed: (1) a superior rate of biomass accumulation. (2) a superior rate of actual yield accumulation in order to acquire a high harvest index, and (3) a time to harvest maturity that is neither shorter nor longer than the duration of the growing season. That duration is provided by the environment, which is the fourth major determinant of yield. Simultaneous selection is required because genetically established interconnections among the three major physiological components cause: (a) a correlation between the harvest index and days to maturity that is usually negative; (b) a correlation between the harvest index and total biomass that is often negative, and (c) a correlation between biomass and days to maturity that is usually positive. All three physiological components and the correlations among them can be quantified by yield system analysis (YSA) of yield trials. An additive main effects and multiplicative interaction (AMMI) statistical analysis can separate and quantify the genotype × environment interaction (G × E) effect on yield and on each physiological component that is caused by each genotype and by the different environment of each yield trial. The use of yield trials to select parents which have the highest rates of accumulation of both biomass and yield, in addition to selecting for the G × E that is specifically adapted to the site can accelerate advance toward the highest potential yield at each geographical site. Higher yield for many sites will raise average regional yield. Higher yield for multiple regions and continents will raise average yield on a world-wide basis. Genetic and physiological bases for lack of indirect selection for biomass from exclusive selection for yield are explained.

Contributions of the Bean/Cowpea CRSP to cultivar and germplasm development in common bean

Disease and abiotic stress are important factors limiting bean production wherever beans are grown. The development of bean cultivars having resistance to these stresses is a cost-effective and sustainable means to address these constraints. During the past 20 years, the Bean/Cowpea Collaborative Research Support Project (B/C CRSP) has supported common bean cultivar development and germplasm improvement programs in the USA and developing countries. Plant breeders have developed and released in Central America and the Caribbean bean cultivars and germplasm with one or more of the following traits; resistance to bean golden yellow mosaic virus (BGYMV), bean common mosaic necrotic virus (BCMNV), rust, web blight and common bacterial blight (CBB) and greater tolerance to high temperatures. In the highlands of Mexico and Ecuador bean cultivars with resistance to anthracnose, rust, root rots and bean common mosaic virus (BCMV), greater biological nitrogen fixation and improved adaptation to intermittent drought have been released. The bean breeding programs in East Africa have developed and released bean cultivars and germplasm with resistance to BCMNV, rust and bruchid seed weevils. Participation in the B/C CRSP has permitted USA bean breeding programs to develop and release bean cultivars and germplasm with resistance to BGYMV, BCMNV, anthracnose, rust, CBB, architectural avoidance to white mold and greater yield potential. Numerous plant breeders, plant pathologists and agronomists from developing countries have received advanced degree training in the USA, which has enhanced the capacity to develop improved bean cultivars for Latin America and Africa. The lack of sustainable seed production and delivery systems continues to limit the impact of the release of improved bean cultivars in many parts of Latin America and East Africa.

Contributions of the Bean/Cowpea CRSP to management of bean diseases

Abstract Diseases are a major constraint to production of beans in developing countries, reducing yields and seed quality. Contributing factors include poor disease management, lack of resistant cultivars, and the limited availability of certified disease-free seed. From the outset the Bean/Cowpea Collaborative Research Support Program (CRSP) has emphasized integrated disease management, and breeding for resistance to bean rust ( Uromyces appendiculatus ), common bacterial blight ( Xanthomonas campestris (= X. axonopodis ) pv. phaseoli ) (CBB) and web blight ( Thanatephorus cucumeris (anamorph Rhizoctonia solani )) (WB). Later in the 1990s, angular leaf spot ( Phaeoisariopsis griseola ) (ALS), and virus induced bean common mosaic (BCM) and bean common mosaic necrosis (BCMN) became more widespread and epidemic. The research included development of disease-resistant germplasm and studies of pathogenic variation and epidemiology. During the early 1990s bean golden yellow mosaic (BGYM), became a major disease of common bean in the Caribbean and Central America. No cultivar resistant to the gemini virus causing BGYM was available in the Dominican Republic (DR) and pesticides were used to reduce transmission of the virus by white flies ( Bremisia tabaci ) biotype A. A change in the bean-production system to limit reproduction of the vector through a host-free period and concentrate the bean growing season to a four month period reduced BGYM significantly. Improved resistant cultivars and disease management resulted in high yields and self-sufficiency of beans in the DR. Evidence for co-evolution of the pathogens causing ALS, CBB, and rust in the two major bean gene pools (Andean and Middle American) was found. Variation in the WB pathogen on bean indicated independent genetic populations and the presence of different anastosmosis subgroups. WB disease management practices should be designed for the sub-group of the pathogen. Seed transmission was found to be a significant source of R. solani inoculum. Specific ( Ur-9 gene) and adult-plant resistance ( Ur-12 gene) to rust was identified for PC-50 (Andean origin) in the DR, and the genes were mapped. A mobile rust nursery was developed to monitor races of rust in a region and assist in resistance-gene deployment in bean germplasm and varieties. DNA based diagnostic methods were developed to differentiate X. campestris pv. phaseoli from X. campestris pv. phaseoli var fuscans (prevalent in East Africa) and P. griseola isolates. DNA hybridization methods also were developed to identify BGYM and bean golden mosaic viruses. Research in USA and East Africa has helped define bean common mosaic virus (BCMV) and bean common mosaic necrotic virus (BCMNV) as separate viruses and has demonstrated that BCMNV appears to be indigenous to Africa. Serological tools were developed that assist in the detection and identification of potyviruses, BCMV and BCMNV. These tools are now used worldwide.

Improvement of Large-Seeded Race Nueva Granada Cultivars

Most large-seeded dry bean (Phaseolus vulgaris L.) of Andean origin are grown in North America, South America, Europe, Asia, and Africa. This wide geographic distribution has generated new gene combinations that favor adaptation to diverse environments (CIAT, 1996). Large-seeded determinate type I and indeterminate type II and III beans include seed types from the Nueva Granada and Chile races (Singh et al., 1991). Popular seed types include dark and light red kidney, red mottled, cranberry, Canario, Azufrado, and large white beans. The seed size of these Andean beans ranges from 30 to 40 g 100-1 seed in warmer climates such as the Caribbean to 50 to 60 g 100-1 for beans grown in temperate and other cooler environments.

Dominant gene for common bean resistance to common bacterial blight caused by Xanthomonas axonopodis pv. phaseoli

The common bacterial blight pathogen [Xanthomonas axonopodis pv. phaseoli (Xap)] is a limiting factor for common bean (Phaseolus vulgaris L.) production worldwide and resistance to the pathogen in most commercial cultivars is inadequate. Variability in virulence of the bacterial pathogen has been observed in strains isolated from Puerto Rico and Central America. A few common bean lines show a differential reaction when inoculated with different Xap strains, indicating the presence of pathogenic races. In order to study the inheritance of resistance to common bacterial blight in common bean, a breeding line that showed a differential foliar reaction to Xap strains was selected and was crossed with a susceptible parent. The inheritance of resistance to one of the selected Xap races was determined by analysis of segregation patterns in the F1, F2, F3 and F4 generations from the cross between the resistant parent PR0313-58 and the susceptible parent ‘Rosada Nativa’. The F1, F2 and F3 generations were tested under greenhouse conditions. Resistant and susceptible F3:4 sister lines were tested in the field. The statistical analysis of all generations followed the model for a dominant resistance gene. The resistant phenotype was found to co-segregate with the SCAR SAP6 marker, located on LG 10. These results fit the hypothesis that resistance is controlled by a single dominant gene. The symbol proposed for the resistance gene is Xap-1 and for the bacterial race, XapV1.

Effect of photoperiod and temperature on common blight disease of common beans (Phaseolus vulgaris L.)

SummaryAlthough common blight disease is serious in many dry bean production areas, there is only limited information on the influence of photoperiod on the disease. Experiments were conducted in growth chambers and in the field (Nebraska, Dominican Republic, Puerto Rico) to investigate the influence of photoperiod × temperature and photoperiod, respectively, on the reaction of cultivars/lines to the causal bacterium Xanthomonas campestris pv. phaseoli. A split-plot design was used in all experiments except in the DR experiment where cultivars/lines were replicated within each photoperiod treatment. The disease reactions were more severe on cultivars/lines under short photoperiod and under higher temperature than under longer photoperiod and lower temperature in the growth chamber. Disease reactions were also more severe under the short photoperiod in the field experiments. No interactions were detected among these factors. These results have important implications for plant breeders in the evaluation of common blight disease reactions in different latitudes.

Nutritional composition and cooking characteristics of tepary bean (Phaseolus acutifolius Gray) in comparison with common bean (Phaseolus vulgaris L.)

Tepary bean is a highly abiotic stress tolerant orphan crop for which there has been limited research on its nutritional value and cooking characteristics. These are key aspects when considering the potential for broader adoption of tepary bean. Therefore, the goal of this study was to evaluate a large set of seed composition and cooking traits related to human nutrition using both landraces and breeding lines of domesticated tepary bean from replicated field trials and to compare the traits in tepary with those in common bean. Tepary bean showed reduced fat and ash concentration and higher sucrose concentration as compared to common bean. Of the twelve amino acids evaluated, only proline in one of the two trials was statistically different between the two species. There were statistically significant differences between tepary and common bean for the concentration of some elements in this study; however, the elemental concentrations fell within the range of those found for common bean in previous studies. The majority of tepary bean lines showed consistently short cooking times and a high percentage of seeds showed measurable water uptake, while some showed a hardshell trait (low water uptake) and longer cooking times. Principal component analysis on a subset of traits showed a distinct group of common beans and two tepary bean groups that were divided on the basis of several agronomic, cooking, and elemental composition traits. Tepary bean, as with other pulses, is a highly nutritious crop with the range of composition and cooking characteristics similar to those of common bean. The variability for seed composition and cooking traits found within tepary bean can be exploited for its improvement.

Isolates of Rhizoctonia solani Can Produce both Web Blight and Root Rot Symptoms in Common Bean (Phaseolus vulgaris L.)

In common bean (Phaseolus vulgaris L.), Rhizoctonia solani Kühn is an important pathogen causing web blight (WB) in the tropics, and it is also a soilborne pathogen causing root rot (RR) worldwide. This pathogen is a species complex classified into 14 anastomosis groups (AG). AG 1-IA, AG 1-IB, AG 1-IE, AG 1-IF, AG 2-2, and AG 4 have been reported to cause WB of the aboveground structures of the plant, while AG 4 and AG 2-2 have been associated with RR. There is limited information, however, concerning the ability of particular isolates of specific AG to cause both diseases in common bean. Nine R. solani isolates, including three AG 1 and three AG 4 WB isolates and three AG 4 RR isolates collected from both leaves and roots, respectively, of common bean in Puerto Rico, were used to evaluate the response of 12 common bean genotypes to WB inoculated using a detached-leaf method and to RR inoculated using a solution suspension of R. solani mycelia in the greenhouse. All R. solani isolates were able to induce both RR and WB symptoms. RR readings were generally more severe than the WB readings. The RR isolate RR1 (AG 4) produced the most severe RR scores. A few bean lines had mean RR scores ≤4.4 for specific R. solani isolates on a scale of 1 to 9, with 1 representing resistant and 9 highly susceptible. However, all of the bean lines had mean RR scores ≥5.0 when inoculated with the isolates RR1, RR2, and RR3, which were determined to be AG 4 in this study. Significant line-isolate interactions were observed for the WB and RR inoculations for the three planting dates, suggesting a differential response of the common bean lines to the pathogen. This genotypic interaction may require bean breeders and pathologists to monitor the virulence patterns of R. solani in specific growing environments, while the compatibility of specific R. solani isolates to both aerial and root tissue needs to be considered for disease control strategies.

ANALYSIS OF GENOTYPE-BY-ENVIRONMENT INTERACTION WITH AMMI MODELS USING SAS PROC MIXED

Genotype-by-environment (GE) interaction can be analyzed using different approaches. Among these, the additive main effects and multiplicative interaction model yields useful interpretations and can be applied successfully to plant breeding programs. In this paper we review fitting strategies for this model and show how to combine the capabilities of the Mixed and IML procedures in SAS to fit this model. This permits straightforward use of likelihood-based inference in standard and non standard situations like complex experimental designs. The proposed procedures were applied to data from red mottled bean variety trials conducted in the Dominican Republic and Puerto Rico in 9 environments with 30 lines (15 with indeterminate and 15 with determinate growth habit).

Development of a QTL-environment-based predictive model for node addition rate in common bean

Key messageThis work reports the effects of the genetic makeup, the environment and the genotype by environment interactions for node addition rate in an RIL population of common bean. This information was used to build a predictive model for node addition rate.AbstractTo select a plant genotype that will thrive in targeted environments it is critical to understand the genotype by environment interaction (GEI). In this study, multi-environment QTL analysis was used to characterize node addition rate (NAR, node day− 1) on the main stem of the common bean (Phaseolus vulgaris L). This analysis was carried out with field data of 171 recombinant inbred lines that were grown at five sites (Florida, Puerto Rico, 2 sites in Colombia, and North Dakota). Four QTLs (Nar1, Nar2, Nar3 and Nar4) were identified, one of which had significant QTL by environment interactions (QEI), that is, Nar2 with temperature. Temperature was identified as the main environmental factor affecting NAR while day length and solar radiation played a minor role. Integration of sites as covariates into a QTL mixed site-effect model, and further replacing the site component with explanatory environmental covariates (i.e., temperature, day length and solar radiation) yielded a model that explained 73% of the phenotypic variation for NAR with root mean square error of 16.25% of the mean. The QTL consistency and stability was examined through a tenfold cross validation with different sets of genotypes and these four QTLs were always detected with 50–90% probability. The final model was evaluated using leave-one-site-out method to assess the influence of site on node addition rate. These analyses provided a quantitative measure of the effects on NAR of common beans exerted by the genetic makeup, the environment and their interactions.