Specification effects in zero tillage survey data in South Asia’s rice-wheat systems

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Published in Field Crops Research 111(1-2): 166-172

Specification effects in zero tillage survey data in South Asia’s rice–wheat systems

Olaf Erenstein

Specification effects in terms of how technology options are contrasted can introduce bias in impact assessment. In a companion paper we evaluated the on-farm impacts of zero tillage (ZT) wheat as a resource-conserving technology in the rice–wheat systems of India’s Haryana State and Pakistan’s Punjab province [Erenstein, O., Farooq, U., Malik, R.K., Sharif, M., 2008. On-farm impacts of zero tillage wheat in South Asia’s rice–wheat systems. Field Crop Res. 105, 240–252]. The underlying field work surveyed plots of full adopters (only ZT plots), partial adopters (ZT and conventional tillage [CT] plots on same farm) and non-adopters (only CT plots). The companion paper assumes that the comparison between the ZT plots of full plus partial adopters and CT plots of partial adopters is the least-biased assessment of ZT’s on-farm impact. Here we revisit this underlying assumption and draw on complementary farm survey findings to illustrate the extent of specification effects in the assessment of on-farm impacts of ZT wheat in the same study areas. The study thereby distinguishes between three contrasts between ZT and CT within the same dataset: (1) plain contrast (all plots of adopters and non-adopters); (2) adopter-only contrast (full and partial adopters only, as used in Erenstein et al. [Erenstein, O., Farooq, U., Malik, R.K., Sharif, M., 2008. On-farm impacts of zero tillage wheat in South Asia’s rice–wheat systems. Field Crop Res. 105, 240–252]); (3) pair-wise contrast (partial adopters only). Proceeding from type 1 to type 3 comparisons the number of observations decrease but this is compensated by an increasing ability to control for variation. The ability of type 3 comparisons to pick up relatively small but significant differences is an important consideration in farm survey impact assessment. However, there is also an increase in partial adoption bias and further follow-up studies are needed to understand the implications of this. The comparisons show that the ZT effects on savings for diesel, tractor time and cost for wheat cultivation are particularly robust. In Haryana ZT’s positive implications for yield and the other financial indicators were also statistically robust, but in Punjab these were sensitive to specification effects. Particularly sensitive to specification effects were the ZT effects on the productivity of applied water in both sites.

Field resistance to spot blotch is not associated with undesirable physio-morphological traits in three spring wheat populations

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Published in Journal of Plant Pathology, 91 (1): 113-122

Field resistance to spot blotch is not associated with undesirable physio-morphological traits in three spring wheat populations

U.R. Rosyara, K. Khadka, S. Subedi, R.C. Sharma and E. Duveiller

Spot blotch, caused by Cochliobolus sativus (Ito and Kurbayzshi) Drechsler ex Dastur is a serious constraint to production of wheat (Triticum aestivum L.) in tropical and sub-tropical environments. Previous efforts to develop genotypes with high levels of resistance combined with other desirable agronomic features have been unsuccessful. This failure was assumed to be largely due to the association of undesirable characters with heightened resistance but information on the existence of such associations is limited. Recently, high levels of resistance have been reported in CIMMYT synthetic wheat genotypes. Our study was done on three populations derived from the spot blotch resistant genotypes ‘Milan/Shanghai #7’, ‘Chirya. 3’ and ‘NL 971’ crossed with the susceptible commercial cultivar ‘BL1473’. Fifteen different physio-morphological traits and areas under disease progress curves (AUDPC) were evaluated in F2 and F3 generations during 2005-2006 at Rampur (Chitwan, Nepal). The majority of traits showed weak negative significant or non-significant genetic and phenotypic correlation with AUDPC except Area Under SPAD (soil plant analysis development) decline curve (AUSDC) and flag leaf duration Results showed no undesirable genetic association of resistance with physiomorphological characters, and thus independent selection for individual traits is possible. In addition, AUSDC and flag leaf duration have potential application as complementary traits in selecting for high resistance.

Phenotypic plasticity of yield and phenology in wheat, sunflower and grapevine

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Published in Field Crops Reseach 110(3): 242-250

Phenotypic plasticity of yield and phenology in wheat, sunflower and grapevine

V.O. Sadras, M.P. Reynolds, A.J. de la Vega, P.R. Petrie and R. Robinson

Abstract:  This paper focuses on the interaction between genotype and environment, a critical aspect of plant breeding, from a physiological perspective. We present a theoretical framework largely based on Bradshaw’s principles of phenotypic plasticity (Adv. Gen. 13: 115) updated to account for recent developments in physiology and genetics. Against this framework we discuss associations between plasticity of yield and plasticity of phenological development. Plasticity was quantified using linear models of phenotype vs environment for 169 wheat lines grown in 6 environments in Mexico, 32 sunflower hybrids grown in at least 15 environments in Argentina and 7 grapevine varieties grown in at least 14 environments in Australia.

In wheat, yield ranged from 0.6 to 7.8 t ha−1 and the range of plasticity was 0.74–1.27 for yield and 0.85–1.17 for time to anthesis. The duration of the post-anthesis period as a fraction of the season was the trait with the largest range of plasticity, i.e. 0.47–1.80. High yield plasticity was an undesirable trait as it was associated with low yield in low-yielding environments. Low yield plasticity and high yield in low-yielding environments were associated with three phenological traits: early anthesis, long duration and low plasticity of post-anthesis development.

In sunflower, yield ranged from 0.5 to 4.9 t ha−1 and the range of plasticity was 0.72–1.29 for yield and 0.72–1.22 for time to anthesis. High yield plasticity was a desirable trait as it was primarily associated with high yield in high-yielding environments. High yield plasticity and high yield in high-yielding environments were associated with two phenological traits: late anthesis and high plasticity of time to anthesis.

In grapevine, yield ranged from 1.2 to 18.7 t ha−1 and the range of plasticity was 0.79–1.29 for yield, 0.86–1.30 for time of budburst, 0.84–1.18 for flowering, and 0.78–1.16 for veraison. High plasticity of yield was a desirable trait as it was primarily associated with high yield in high-yielding environments. High yield plasticity was associated with two phenological traits: plasticity of budburst and plasticity of anthesis.

We report for the first time positive associations between plasticities of yield and phenology in crop species. It is concluded that in addition to phenology per se (i.e. mean time to a phenostage), plasticity of phenological development merits consideration as a distinct trait influencing crop adaptation and yield.

Rapid gains in yield and adoption of new maize varieties for complex hillside environments through farmer participation. II. Scaling-up the adoption through community-based seed production (CBSP)

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Published in Field Crops Research 111(1-2): 144-151
Rapid gains in yield and adoption of new maize varieties for complex hillside environments through farmer participation. II. Scaling-up the adoption through community-based seed production (CBSP)
 
T.P. Tiwari, G. Ortiz-Ferrara, C. Urrea, R.B. Katuwal, K.B. Koirala, R.C. Prasad, D.B. Gurung, D. Sharma, B. Hamal, B. Bhandari and M. Thapa.
 
Abstract:  Participatory varietal selection (PVS) led to the identification of Population-22 and its later release as Manakamana-3. Subsequently further mother–baby trials tested five unreleased open-pollinated varieties (OPVs), ZM-621, Shitala, Population-45, Hill Pool White, and Hill Pool Yellow to compare them with Manakamana-3. Farmers again preferred Manakamana-3 as well as ZM-621 for their stable, higher grain yield, and for other traits such as stay-green, non-lodging, large white grains, and tolerance to foliar diseases. However, Manakamana-3 and ZM-621 both had late maturity, open husks and dented grain. Both were tested with farmers on-farm co-ordinated farmers field trials (CFFTs) and had not been identified as this was more contractual type of participatory research. Individual traits were measured but overall farmers’ preferences were not elicited. In the more collaborative participation of the mother–baby trials the overall preference was determined and farmers traded-off the late maturity and dented grains of Manakamana-3 and ZM-621 against other favourable traits. Depending on location, these genotypes yielded 15–45% more grain than the local varieties in the mother–baby trials. These results led to the release of ZM-621 as Deuti in 2006. Farmers had adopted Manakamana-3 (released in 2002) and ZM-621 (Deuti) as a direct result of PVS trials and increased area under them year after year. Farmers awareness of the varieties has increased and seeds of these varieties are under community-based seed production (CBSP). Involving farmers through a collaborative mode of participation in varietal selection overcame bottlenecks to finding new varieties that had occurred with more contractual on-farm research.

 

Specification effects in zero tillage survey data in South Asia’s rice–wheat systems

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Published in Field Crops Research 111(1-2): 166-172

Specification effects in zero tillage survey data in South Asia’s rice–wheat systems

Olaf Erenstein

Abstract:  Specification effects in terms of how technology options are contrasted can introduce bias in impact assessment. In a companion paper we evaluated the on-farm impacts of zero tillage (ZT) wheat as a resource-conserving technology in the rice–wheat systems of India’s Haryana State and Pakistan’s Punjab province [Erenstein, O., Farooq, U., Malik, R.K., Sharif, M., 2008. On-farm impacts of zero tillage wheat in South Asia’s rice–wheat systems. Field Crop Res. 105, 240–252]. The underlying field work surveyed plots of full adopters (only ZT plots), partial adopters (ZT and conventional tillage [CT] plots on same farm) and non-adopters (only CT plots). The companion paper assumes that the comparison between the ZT plots of full plus partial adopters and CT plots of partial adopters is the least-biased assessment of ZT’s on-farm impact. Here we revisit this underlying assumption and draw on complementary farm survey findings to illustrate the extent of specification effects in the assessment of on-farm impacts of ZT wheat in the same study areas. The study thereby distinguishes between three contrasts between ZT and CT within the same dataset: (1) plain contrast (all plots of adopters and non-adopters); (2) adopter-only contrast (full and partial adopters only, as used in Erenstein et al. [Erenstein, O., Farooq, U., Malik, R.K., Sharif, M., 2008. On-farm impacts of zero tillage wheat in South Asia’s rice–wheat systems. Field Crop Res. 105, 240–252]); (3) pair-wise contrast (partial adopters only). Proceeding from type 1 to type 3 comparisons the number of observations decrease but this is compensated by an increasing ability to control for variation. The ability of type 3 comparisons to pick up relatively small but significant differences is an important consideration in farm survey impact assessment. However, there is also an increase in partial adoption bias and further follow-up studies are needed to understand the implications of this. The comparisons show that the ZT effects on savings for diesel, tractor time and cost for wheat cultivation are particularly robust. In Haryana ZT’s positive implications for yield and the other financial indicators were also statistically robust, but in Punjab these were sensitive to specification effects. Particularly sensitive to specification effects were the ZT effects on the productivity of applied water in both sites.

New article from CIMMYT – Estimating maize genetic erosion in modernized smallholder agriculture

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Published in Theoretical and Applied Genetics 119(5): 875-888 (2009)

Estimating maize genetic erosion in modernized smallholder agriculture

Joost van Heerwaarden, J. Hellin, R. F. Visser and F. A. van Eeuwijk

Abstract: Replacement of crop landraces by modern varieties is thought to cause diversity loss. We studied genetic erosion in maize within a model system; modernized smallholder agriculture in southern Mexico. The local seed supply was described through interviews and in situ seed collection. In spite of the dominance of commercial seed, the informal seed system was found to persist. True landraces were rare and most informal seed was derived from modern varieties (creolized). Seed lots were characterized for agronomical traits and molecular markers. We avoided the problem of non-consistent nomenclature by taking individual seed lots as the basis for diversity inference. We defined diversity as the weighted average distance between seed lots. Diversity was calculated for subsets of the seed supply to assess the impact of replacing traditional landraces with any of these subsets. Results were different for molecular markers, ear- and vegetative/flowering traits. Nonetheless, creolized varieties showed low diversity for all traits. These varieties were distinct from traditional landraces and little differentiated from their ancestral stocks. Although adoption of creolized maize into the informal seed system has lowered diversity as compared to traditional landraces, genetic erosion was moderated by the distinct features offered by modern varieties.

New article from CIMMYT – Raising yield potential in wheat

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Published in Journal of Experimental Botany 60(7):1899-1918 (2009)

Raising yield potential in wheat

Matthew Reynolds, M. John Foulkes, Gustavo A. Slafer, Peter Berry, Martin A. J. Parry, John W. Snape and William J. Angus.

Abstract. Recent advances in crop research have the potential to accelerate genetic gains in wheat, especially if co-ordinated with a breeding perspective. For example, improving photosynthesis by exploiting natural variation in Rubisco’s catalytic rate or adopting C4 metabolism could raise the baseline for yield potential by 50% or more. However, spike fertility must also be improved to permit full utilization of photosynthetic capacity throughout the crop life cycle and this has several components. While larger radiation use efficiency will increase the total assimilates available for spike growth, thereby increasing the potential for grain number, an optimized phenological pattern will permit the maximum partitioning of the available assimilates to the spikes. Evidence for underutilized photosynthetic capacity during grain filling in elite material suggests unnecessary floret abortion. Therefore, a better understanding of its physiological and genetic basis, including possible signalling in response to photoperiod or growth-limiting resources, may permit floret abortion to be minimized for a more optimal source:sink balance. However, trade-offs in terms of the partitioning of assimilates to competing sinks during spike growth, to improve root anchorage and stem strength, may be necessary to prevent yield losses as a result of lodging. Breeding technologies that can be used to complement conventional approaches include wide crossing with members of the Triticeae tribe to broaden the wheat genepool, and physiological and molecular breeding strategically to combine complementary traits and to identify elite progeny more efficiently.

New article from CIMMYT – Biplot Analysis of Genotype x Environment Interaction: Proceed with Caution

Posted by Petr Kosina on , in Journal Articles

Published in Crop Sci 49:1564-1576 (2009)

Biplot Analysis of Genotype x Environment Interaction: Proceed with Caution

Rong-Cai Yang, Jose Crossa, Paul L. Cornelius and Juan Burgueño

Abstract: Biplot analysis has been used for studying genotype x environment interaction (GE) or any two-way table. Its descriptive and visualization capabilities along with the availability of user-friendly software have enabled plant scientists to examine any two-way data by a click on a computer button. Despite widespread use, the validityand limitations of biplot analysis have not been completely examined. Here we identify and briefly discuss six key issues surrounding overutilization or abuse of biplot analysis. We question (i) whether the retention of the first two multiplicative terms in the biplot analyses is adequate; (ii) whether the biplot can be more than a simple descriptive technique; (iii) how realistic a “which-won-where” pattern is identified from a biplot; (iv) what if genotypes and/or environments are random effects; (v) how relevant biplot analysis is to the understanding of the nature and causes of interaction; and (vi) how much the biplot analysis can contribute to detection of crossover interaction. We stress the need for use of confidence regions for individual genotype and environment scores in biplots to make critical decisions on genotype selection or cultivar recommendation based on a statistical test. We conclude that the biplot analysis is simply a visually descriptive statistical tool and researchers should proceed with caution if using biplot analysis beyond this simple function.

New article from CIMMYT – Mega-Environment Identification for Barley Based on Twenty-Seven Years of Global Grain Yield Data

Posted by Petr Kosina on , in Journal Articles

Published in Crop Sci 49:1705-1718 (2009)

Mega-Environment Identification for Barley Based on Twenty-Seven Years of Global Grain Yield Data

Eduardo Hernandez-Segundo, Flavio Capettini, Richard Trethowan, Maarten van Ginkel, Apolinar Mejia, Aquiles Carballo, Jose Crossa, Mateo Vargas andArtemio Balbuena-Melgarejo

Abstract: Knowledge of target environments in breeding programs is important to better direct the development of germplasm. The objectives of this study were to identify associations among barley (Hordeum vulgare L.) growing environments to identify mega-environments to select the best locations to breed barley. Twenty-seven years of grain yield data from the International Barley Yield Trial (IBYT) conducted by the ICARDA-CIMMYT Barley Breeding Program, consisting of 750 grain yield trials of two replications representing 235 locations in 75 countries, were analyzed using pattern analysis to group sites across years that represent similar selection environments. The shifted multiplicative model (SHMM) was employed to group sites within each year. Environments clustered into three main groups and squared Euclidean distances were used to identify a representative location within each cluster. Group 1 locations were characterized as being cool with intermediate precipitation; Group 2 locations were warmer and drier; and Group 3 sites were generally cool and had the highest average precipitation. The respective representative key locations for each of the three groups were Leida, Spain; Boulifa, Tunisia; and Setif, Algeria. All three key locations are located in the Northern Hemisphere between 36° and 41° latitude. Theresults of this study show that the global adaptation of barley is possible and can be improved by breeding and selection for adaptation within the three main mega-environments identified.