Suitability of mapped sequence tagged microsatellite site markers for establishing distinctness, uniformity and stability in aromatic rice

At present, testing for distinctness, uniformity and stability (DUS) of crop varieties relies on a set of morphological characters. These characters suffer fromthe limitations of number, interaction with the environment in which the variety grows and subjectivity in decision-making. The potential of DNA-based markers such as sequence tagged microsatellite site (STMS), for establishing DUS merits investigation. In the present study, a set of 55 mapped STMS markers, selected from 12 linkage groups of rice genome, was used to examine distinctness of 23 aromatic rice genotypes including the commercially important Basmati varieties. Forty-one of these markers (74.5%) showed polymorphism between the varieties. The number of alleles per locus ranged from 2–4 with an average of 2.3. The polymorphism information content (PIC) of the markers varied from 0.083 to 0.665 with an average of 0.338. All the varieties could be differentiated from each other at a low probability (0.07×10^-13) of identical match by chance. The marker-based clustering of the varieties corresponded with the known phenotypic classification, thereby providing confidence in the distinctness established by the mapped STMS markers. The utility of these markers to study uniformity and stability was analysed using a commercially important crossbred Basmati rice variety Pusa Basmati 1(IET-10364) that contributes about 40–50% of Basmati rice export from India. Genotyping of twenty individual plants, grown from the nucleus, breeder, foundation, certified and farmer's saved seed samples using all the 55 markers revealed no variation among the plants. These observations suggested that the set of mapped markers employed in this study could be further used for establishing distinctness of aromatic rice varieties and for studying DUS of the important commercial variety Pusa Basmati 1. This revised version was published online in July 2006 with corrections to the Cover Date.     

Heterosis,molecular diversity,combining ability and their interrelationships in short duration maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) across the environments

Five inbred lines, 10 single cross maize (Zea mays L.) hybrids and two standard cultivars as check were used to study the combining abilities and heterosis under three environmental conditions. Random amplified polymorphic DNAs (RAPDs) markers were used to study the genetic diversity (GD) and further to analyze relationship of RAPDs based GD with combining ability and heterosis in short duration maize. Spearman’s rank correlation coefficients and linear regressions were analyzed to identify the most important factor determining heterosis and per se performance of the hybrids. Variances due to general combining ability (GCA), specific combining ability (SCA) and their interactions with environment were found to be significant. Twenty random primers generated 179 RAPD fragments. Of these, 102 RAPD fragments were polymorphic. GD was determined using Jaccard’s similarity coefficient, and a dendogram was constructed by UPGMA cluster analysis. The RAPDs based GD exhibited non-significant negative or positive association, non-significant linear regression along with very low coefficient of determination (R ²) with SCA, high and mid parent heterosis (HP and MP) and per se performance of the hybrids. Significant positive correlations and regressions along with high coefficients of determination were recorded for SCA with HP, MP and per se performance of the hybrids. The HP and MP also established significant positive association and linear regression along with high coefficient of determination with per se performance of hybrids whereas the parental mean did not establish any significant correlations with the GD, HPH, MPH and grain yield of F₁s. The present investigation, therefore, did not find any role of RAPDs based GD in determining hybrid heterosis and hybrid performance in short duration sub-tropical maize. The SCA, however, has emerged as the most important factor in determination of heterosis as well as per se performance of the hybrids in short duration maize.     

Global status of wheat leaf rust caused by <Emphasis Type="Italic">Puccinia triticina</Emphasis>

Leaf rust caused by Puccinia triticina is the most common and widely distributed of the three wheat rusts. Losses from leaf rust are usually less damaging than those from stem rust and stripe rust, but leaf rust causes greater annual losses due to its more frequent and widespread occurrence. Yield losses from leaf rust are mostly due to reductions in kernel weight. Many laboratories worldwide conduct leaf rust surveys and virulence analyses. Most currently important races (pathotypes) have either evolved through mutations in existing populations or migrated from other, often unknown, areas. Several leaf rust resistance genes are cataloged, and high levels of slow rusting adult plant resistance are available in high yielding CIMMYT wheats. This paper summarizes the importance of leaf rust in the main wheat production areas as reflected by yield losses, the complexity of virulence variation in pathogen populations, the role cultivars with race-specific resistance play in pathogen evolution, and the control measures currently practiced in various regions of the world.     

Genotypic variability in vegetable amaranth (Amaranthus tricolor L for foliage yield and its contributing traits over successive cuttings and years

Summary Twenty nine strains of vegetable amaranth (Amaranthus tricolor were grown for two successive seasons to study different selection parameters for foliage yield and its nine contributing morphological and quality traits. The strains AV-38 (5.06 kg/plot) and AV-31 (5.04 kg/plot) recorded highest foliage yield, followed by AV-30 (4.78 kg/plot) and AV-23 (4.70 kg/plot). The protein and carotenoid content averaged 1.24 ± 0.03 mg/100 mg and 0.83 ± 0.02 mg/g respectively. The leaves of A. tricolor also have considerable quantities of ascorbic acid (112.33 ± 5.00 mg/100 g) and fibre (8.39 ± 0.10%). The mean of individual cuttings for plant height, leaf size, stem diameter, foliage yield, protein, ascorbic acid and fibre content increased with successive cuttings till third cutting and thereafter showed a decline. Genotypic coefficient of variation (GCV) values ranged from 6.80 to 28.25%. However, the fibre content, branches/plant, leaves/plant, plant height and stem diameter showed lowest values of GCV. The values of heritability estimates were high for all the traits in all the cuttings as well as on pooled basis and ranged from 0.89 for branches/plant to 0.98 for foliage yield. Highest expected genetic advance was noticed for ascorbic acid (57.48%), followed by foliage yield (48.30%) and leaf size (29.51%).     

Trend and Stability Analysis to Interpret Results of Long-Term Effects of Application of Fertilizers and Manure to Cotton Grown on Rainfed Vertisols

A field experiment was conducted from 1985–1986 to 2002–2003 on Vertisols under rainfed conditions to evaluate the effect of cropping systems and application of fertilizers and manure on seed cotton yield. To determine the long‐term effects, trends and stability analyses were performed. Soil samples (0–0.15 and 0.15–0.30 m) were collected at the end of year 18 and analysed for available P and AB‐DTPA extractable Zn. Among cropping systems, Asiatic diploid cotton (Gossypium arboreum) yielded 233 kg ha^?1 more seed cotton than the upland tetraploid cotton (Gossypium hirsutum). Yield trend was positive for G. arboreum compared with G. hirsutum. However, the slope was not significant. Stability analyses indicated overall higher yield stability for G. arboreum than G. hirsutum. Compared with monocropping G. hirsutum, G. hirsutum–sorghum (Sorghum bicolor L.) (H‐S) rotation was significantly more stable. Soil samples (0–0.30 m) of the manure‐amended plots had significantly greater P and Zn content (above the critical limit) compared to those receiving inorganic fertilizers alone. With regard to nutrient management practices, seed cotton yield was the highest for the integrated nutrient management (INM) treatment receiving a combination of organic and inorganic fertilizers. Among primary nutrients, the effect of P was significant while that of K was not. Balanced fertilizer application was significantly better than treatments receiving N and NK. Yield trends were, in general, not significant. However, a positive trend was noticed for treatments receiving manure compared to fertilizer alone. Stability analysis, on the other hand, indicated that the slopes were, in general, significant. Among the nutrients, mean yield response with and without P was 1007 and 672 kg ha^?1 respectively. Combined application of manure and fertilizer (INM) resulted in the highest mean yield response (1218 kg ha^?1) and the slope was highly significant (P < 0.004). In the manure‐amended plots, a better nutrient status probably imparted a greater degree of yield stability. The present study suggests that compared to trend analysis, stability analysis being sensitive as it recognizes the treatment × environment interaction, is a better option to interpret results from long‐term agronomic experiments.     

Tillage, cover crops, and nitrogen fertilization effects on soil nitrogen and cotton and sorghum yields

Sustainable soil and crop management practices that reduce soil erosion and nitrogen (N) leaching, conserve soil organic matter, and optimize cotton and sorghum yields still remain a challenge. We examined the influence of three tillage practices (no-till, strip till and chisel till), four cover crops {legume [hairy vetch (Vicia villosa Roth)], nonlegume [rye (Secaele cereale L.)], vetch/rye biculture and winter weeds or no cover crop}, and three N fertilization rates (0, 60–65 and 120–130 kg N ha⁻¹) on soil inorganic N content at the 0–30 cm depth and yields and N uptake of cotton (Gossypium hirsutum L.) and sorghum [Sorghum bicolor (L.) Moench]. A field experiment was conducted on Dothan sandy loam (fine-loamy, siliceous, thermic, Plinthic Paleudults) from 1999 to 2002 in Georgia, USA. Nitrogen supplied by cover crops was greater with vetch and vetch/rye biculture than with rye and weeds. Soil inorganic N at the 0–10 and 10–30 cm depths increased with increasing N rate and were greater with vetch than with rye and weeds in April 2000 and 2002. Inorganic N at 0–10 cm was also greater with vetch than with rye in no-till, greater with vetch/rye than with rye and weeds in strip till, and greater with vetch than with rye and weeds in chisel till. In 2000, cotton lint yield and N uptake were greater in no-till with rye or 60 kg N ha⁻¹ than in other treatments, but biomass (stems + leaves) yield and N uptake were greater with vetch and vetch/rye than with rye or weeds, and greater with 60 and 120 than with 0 kg N ha⁻¹. In 2001, sorghum grain yield, biomass yield, and N uptake were greater in strip till and chisel till than in no-till, and greater in vetch and vetch/rye with or without N than in rye and weeds with 0 or 65 kg N ha⁻¹. In 2002, cotton lint yield and N uptake were greater in chisel till, rye and weeds with 0 or 60 kg N ha⁻¹ than in other treatments, but biomass N uptake was greater in vetch/rye with 60 kg N ha⁻¹ than in rye and weeds with 0 or 60 kg N ha⁻¹. Increased N supplied by hairy vetch or 120–130 kg N ha⁻¹ increased soil N availability, sorghum grain yield, cotton and sorghum biomass yields, and N uptake but decreased cotton lint yield and lint N uptake compared with rye, weeds or 0 kg N ha⁻¹. Cotton and sorghum yields and N uptake can be optimized and potentials for soil erosion and N leaching can be reduced by using conservation tillage, such as no-till or strip till, with vetch/rye biculture cover crop and 60–65 kg N ha⁻¹. The results can be applied in regions where cover crops can be grown in the winter to reduce soil erosion and N leaching and where tillage intensity and N fertilization rates can be minimized to reduce the costs of energy requirement for tillage and N fertilization while optimizing crop production.     

Development of Elongated Uppermost Intemode CMS Lines for Hybrid Rice Breeding in India

Development of cytoplasmic male sterile （CMS） lines with elongated uppermost internode （EUI） trait provides a genetic option to eliminate the use of GA3 in hybrid rice. During the past two decades, extensive work has been carried out on the subject that resulted in identification of several mutants with EUI trait for use in developing cytoplasmic/thermo-sensitive genic male-sterile lines with complete panicle exsertion （Okuno and Kawai, 1978; Rutger and Carnahan, 1981; Shen et al., 1987; Yang et al., 2000; 2002; Gangashetti et al., 2004）. Two recessive genes （eui-1 and eui-2） mapped on chromosome 5 and 10 respectively have so far been reported to control the internode elongation in rice （Librojo and Khush, 1986; Yang et al., 2001; Ma et al., 2004）. Considerable progress has been made in China in exploiting ＇eur gene for development of hybrid rice parental lines （Yang et al., 2000; 2002; Zhang et al., 2002）.     

Breeding crops for reduced-tillage management in the intensive, rice–wheat systems of South Asia

The importance of reduced tillage in sustainable agriculture is well recognized. Reduced-tillage practices (which may or may not involve retention of crop residues) and their effects differ from those of conventional tillage in several ways: soil physical properties; shifts in host–weed competition; soil moisture availability (especially when sowing deeply or under stubble); and the emergence of pathogen populations that survive on crop residues. There may be a need for genotypes suited to special forms of mechanization (e.g. direct seeding into residues) and to agronomic conditions such as allelopathy, as well as specific issues relating to problem soils. This article examines issues and breeding targets for researchers who seek to improve crops for reduced-tillage systems. Most of the examples used pertain to wheat, but we also refer to other crops. Our primary claim is that new breeding initiatives are needed to introgress favourable traits into wheat and other crops in areas where reduced or zero-tillage is being adopted. Key traits include faster emergence, faster decomposition, and the ability to germinate when deep seeded (so that crops compete with weeds and use available moisture more efficiently). Enhancement of resistance to new pathogens and insect pests surviving on crop residues must also be given attention. In addition to focusing on new traits, breeders need to assess germplasm and breeding populations under reduced tillage. Farmer participatory approaches can also enhance the effectiveness of cultivar development and selection in environments where farmers’ links with technology providers are weak. Finally, modern breeding tools may also play a substantial role in future efforts to develop adapted crop genotypes for reduced tillage.     

High yielding spring bread wheat germplasm for global irrigated and rainfed production systems

Global wheat (Triticum aestivum L.) production must increase 2% annually until 2020 to meet future demands. Breeding wheat cultivars with increased grain yield potential, enhanced water-use efficiency, heat tolerance, end-use quality, and durable resistance to important diseases and pests can contribute to meet at least half of the desired production increases. The remaining half must come through better agronomic and soil management practices and incentive policies. Analyses of the recent International Yield Trials indicate that grain yields of the best new entries were usually 10% higher than the local checks globally, as well as within a country across sites. Variation in yield across sites within a country/region underline the role of genotype × environment (GE) interaction and provides opportunities to select for stable genotypes, which is not often done. The lack of proper analysis undermines proper utilization of germplasm with high yield potential and stability in the national wheat breeding programs. Some of the best performers in irrigated areas were amongst the best in semiarid environments, reinforcing the fact that high yield potential and drought tolerance can be improved simultaneously. The best performing lines often had genotypic base of widely adapted genotypes Kauz, Attila, Baviacora, and Pastor, with genetic contributions from other parents including synthetic wheat. We recommend within country multilocation analysis of trial performance for a crop season to identify lines suiting particular or different locations within a country. The immediate feedback on GE interaction will also help in breeding lines for countries having substantial variation across locations and years.     

Relationships between height and yield in near-isogenic spring wheats that contrast for major reduced height genes

The effect of two major dwarfing (Rht-B1b and Rht-D1b) genes varies with environment. Near-isogenic pairs (i.e., tall and semidwarf) of six spring wheat lines, included in the International Adaptation Trial (IAT), were grown in 81 trials around the world from 2001 to 2004. Trial yields ranged from 1 to 8 t ha⁻¹ with a mean of ca. 4 t ha⁻¹. Overall, the yield advantage of the lines possessing the dwarfing gene was ca. 10% and was particularly evident in trials where the mean height of semidwarf isolines exceeded ca. 80 cm. However, the yield advantage was greater in the slightly taller and older lines (Pavon and Galvez) than in the newer lines Nesser and Kauz and the two durum lines. Sixteen pairs of semidwarf/tall near-isolines were grown in six managed drought environment trials at CIMMYT in northwestern Mexico. In these trials, height and yield differences were small and/or negligible in the most droughted environment (2.5 t ha⁻¹) and the slope of yield versus height for each isoline pair became consistently negative with increase in irrigation. In the IAT, the slope of the yield versus height was much more variable at low heights or yields, presumably due to the fact that there were many more factors driving the response. Even at the point where the slope became consistently negative (ca. between 2 and 4 t ha⁻¹), there were some trials where tall isolines equaled or exceeded the yield of semidwarf isolines, particularly in the most recent developed cultivar, Kauz. For submission to Euphytica as part of special issue “Challenges to International Wheat Breeding”. From the International Symposium on Wheat Yield Potential: Challenges to International Wheat Breeding, Days Inn, Ciudad Obregón, Sonora, Mexico, March 19–24th, 2006.