Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

Frequency and fertility restoration efficiency of Rf3 and Rf4 genes in Indian rice

Identification of new parental lines is crucial for developing ecology‐specific hybrids with ideal agronomic performance. We screened a total of 570 different ecology‐specific Indian rice varieties for the presence of fertility restorer genes, Rf3 and Rf4 using tightly linked markers DRRM Rf3‐10 and RM6100, respectively. Among these varieties, 13% carried Rf3Rf3/Rf4Rf4, 31% carried rf3rf3/rf4rf4, 6% carried Rf3Rf3/rf4rf4 and remaining 50% carried Rf4Rf4/rf3rf3 allelic combinations. A mini set of 40 varieties with variable allelic combinations of fertility restorer genes were testcrossed with WA and Kalinga‐based CMS lines. All the 80 F₁s were evaluated for spikelet fertility and fertility restoration ability. Rf3Rf3/rf4rf4 genotypes mostly behaved as partial maintainers or partial restorers. In contrast, rf3rf3/Rf4Rf4 genotypes were partial or effective restorers. However, double dominant genotypes showed better fertility restoration than the genotypes containing Rf3 or Rf4 individually. Some of the genotypes showed unexpected restoration pattern implying occurrence of other fertility restorer(s) apart from Rf3 and Rf4. The perfect restorers and maintainers identified in this study can be directly used in hybrid rice breeding.     

Methane emission from two Indian soils planted with different rice cultivars

In a greenhouse study, methane emissions were measured from two diverse Indian rice-growing soils planted to five rice cultivars under similar water regimes, fertilizer applications and environmental conditions. Significant variations were observed in methane emitted from soils growing different cultivars. Total methane emission varied between 8.04 and 20.92gm^–2 from IARI soil (Inceptisol) and between 1.47 and 10.91gm^–2 from Raipur soil (Vertisol) planted to rice. In all the cultivars, emissions from IARI soil were higher than from Raipur soil. The first methane flux peak was noticed during the reproductive phase and the second peak coincided with the grain-ripening stage of the rice cultivars. Received: July 7, 1996     

Heavy Metal Contamination of Soil and Vegetation in the Vicinity of Industries in Bangladesh

Water, Air, &; Soil Pollution - A study was conducted to investigate the heavy metal contamination of soil and vegetation in the vicinity of industries around Dhaka city in Bangladesh....     

Heat-induced aggregation of whey proteins: comparison of cheese WPC with acid WPC and relevance of mineral composition

Heat-induced aggregation of whey proteins in solutions made from two commercial whey protein concentrates (WPCs), one derived from mineral acid whey (acid WPC) and the other from cheese whey (cheese WPC), was studied using polyacrylamide gel electrophoresis (PAGE), size exclusion chromatography (SEC), and transmission electron microscopy (TEM). Heat treatment (75 degrees C) of acid WPC solutions (12.0%, w/w, pH 6.9) resulted in formation of relatively small "soluble" aggregates that were predominantly disulfide-linked. By contrast, heat treatment of the cheese WPC solutions (under the same conditions) caused formation of relatively large aggregates, containing high proportions of aggregates linked by noncovalent associations. The rate of aggregation of both beta-lactoglobulin and alpha-lactalbumin at 75 degrees C, measured as the loss of native proteins by PAGE, was higher in the cheese WPC solution than in the acid WPC solution. Cross dialysis of the two WPC solutions resulted in alteration of the mineral composition of each WPC solution and reversing their heat-induced aggregation behavior. The results demonstrated that the mineral composition is very important in controlling the aggregation behavior of WPC products.     

Effect of Temperature on Bio-Kinetic Coefficients in UASB Treatment of Municipal Wastewater

Upflow anaerobic sludge blanket (UASB)reactors were used to treat municipal wastewater attemperatures of 6, 11, 15, 20 and 32 °C and athydraulic retention times (HRTs) ranging from 48 to 3 h overan operational period of approximately 860 days. The Monodmodel was used to evaluate substrate utilization. TheArrhenius model was used to calculate the activationenergies from which temperature coefficients weredetermined. It was found that the maximum specific substrateutilization rate constant (k) decreased from 0.387 d^-1(at 32 °C) to 0.041 d^-1 (at 6 °C). Thedecay rate constant (k_d), yield coefficient (Y_g),half velocity constant (K_s) and maximum specific growthrate (μ_m ) were also impacted by temperature in theUASB treatment of municipal wastewater.     

Agroforestry techniques for the rehabilitation of degraded salt-affected lands in India

The development of appropriate technologies for the judicious use of India's 8.11 million ha of salt-affected lands would give increased food, fodder and fuelwood production. A sizeable portion of the salt-affected lands of the Indo-Gangetic plain have been reclaimed through chemical amendments and are being commercially used for arable farming. However, large areas of salt-affected common lands, village and government lands and waste lands near cities, along railway tracks and roads do not have any productive use. Owing to their sparse vegetative cover such lands are vulnerable to further degradation and can be a source of runoff causing floods, especially where cows congregate. Research at the Central Soil Salinity Research Institute, Karnal has generated agroforestry techniques which could enable the economic exploitation of such marginal lands. This paper deals with various aspects of these techniques, which have been applied to over 50 000 ha by 1994. Based on eight to ten years of growth and biomass figures, the most salt-tolerant woody species identified were: Prosopis juliflora, Acacia nilotica, Casuarina equisetifolia, Tamarix articulata, Leptochloa fusca (a palatable forage grass which was found to be a promising primary colonizer of salt lands). Agronomic practices for the successful establishment of trees such as planting methods, amendment use, irrigation, spacing and lopping schedules are discussed. A Prosopis juliflora-leptochloa fusca silvipastoral model was found to be excellent for fuelwood and forage production and for the amelioration of high pH soils. This system, when followed for little more than four years, reclaims alkali soils to such an extent that normal agriculture crops such as Trifolium alexandrinum and T. resupinatum can be grown successfully. A ridge-trench system of tree planting was found to be helpful in alkali soils, the in situ rainwater conservation it led to assisting biomass production. Eucalyptus tereticornis, Populus deltoides and Tectona grandis based agroforestry were promising for reclaimed salt-affected lands. The short- and long-term effects of various tree plantations on the physicochemical properties of the soil and on soil-water relations are also discussed. Agroforestry options for the development of salt-affected lands found in various agroclimatic zones of India are explored.     

Geostatistical and fuzzy clustering approach for delineation of site-specific management zones and yield-limiting factors in irrigated hot arid environment of India

Precision Agriculture - Delineation of management zones (MZs) are needed to manage fields in order to maximize economic return, minimize environmental impact, and improve soil and crop management....     

Hydrus-1D model for simulating water flow through paddy soils under alternate wetting and drying irrigation practice

Paddy and Water Environment - Alternate wetting and drying (AWD) irrigation practice in paddy cultivation requires a safe soil moisture stress level in the root zone for which irrigation water...