With the rapid development of DNA technologies, high throughput genomic data have become a powerful leverage to locate desirable genetic loci associated with traits of importance in various crop species. However, curr...With the rapid development of DNA technologies, high throughput genomic data have become a powerful leverage to locate desirable genetic loci associated with traits of importance in various crop species. However, current genetic association mapping analyses are focused on identifying individual QTLs. This study aimed to identify a set of QTLs or genetic markers, which can capture genetic variability for marker-assisted selection. Selecting a set with k loci that can maximize genetic variation out of high throughput genomic data is a challenging issue. In this study, we proposed an adaptive sequential replacement (ASR) method, which is considered a variant of the sequential replacement (SR) method. Through Monte Carlo simulation and comparing with four other selection methods: exhaustive, SR method, forward, and backward methods we found that the ASR method sustains consistent and repeatable results comparable to the exhaustive method with much reduced computational intensity.展开更多
Linear mixed model (LMM) approaches have been widely applied in many areas of research data analysis because they offer great flexibility for different data structures and linear model systems. In this study, emphasis...Linear mixed model (LMM) approaches have been widely applied in many areas of research data analysis because they offer great flexibility for different data structures and linear model systems. In this study, emphasis is placed on comparing the properties of two LMM approaches: restricted maximum likelihood (REML) and minimum norm quadratic unbiased estimation (MINQUE) with and without resampling techniques being included. Bias, testing power, Type I error, and computing time were compared between REML and MINQUE approaches with and without Jackknife technique based on 500 simulated data sets. Results showed that MINQUE and REML methods performed equally regarding bias, Type I error, and power. Jackknife-based MINQUE and REML greatly improved power compared to non-Jackknife based linear mixed model approaches. Results also showed that MINQUE is more time-saving compared to REML, especially with the use of resampling techniques and large data set analysis. Results from the actual cotton data analysis were in agreement with our simulated results. Therefore, Jackknife-based MINQUE approaches could be recommended to achieve desirable power with reduced time for a large data analysis and model simulations.展开更多
Healthy soils are important to ensure satisfactory crop growth and yield. Poultry litter (PL), as an organic fertilizer, has proven to supply the soil with essential macro and micronutrients, enhance soil fertility, a...Healthy soils are important to ensure satisfactory crop growth and yield. Poultry litter (PL), as an organic fertilizer, has proven to supply the soil with essential macro and micronutrients, enhance soil fertility, and improve crop productivity. Integrating this treatment has the potential to improve soil physical and biological properties by increasing soil carbon, C. However, rapid decomposition and mineralization of PL, particularly in the hot and humid southeastern U.S., resulted in losing C and reduced its effect on soil health. Biochar and lignite have been proposed to stabilize and mitigate C loss through application of fresh manure. However, their combined effects with PL on C sequestration and soil health components are limited. A field experiment was conducted on Leeper silty clay loam soil from 2017 to 2020 to evaluate the combined effect on soil properties when applying biochar and lignite with PL to cotton (Gossypium hirsutum L.). The experimental design was a randomized complete block involving nine treatments replicated three times. Treatments included PL and inorganic nitrogen, N, fertilizer with or without biochar and lignite, and an unfertilized control. Application rates were 6.7 Mgkg⋅ha−1</sup> for PL, 6.7 Mgkg⋅ha−1</sup></sup> for biochar and lignite and 134 kg⋅ha−1</sup><sup></sup> for inorganic N fertilizer. Integration of PL and inorganic fertilizer with biochar and lignite, resulted in greater soil infiltration, aggregate stability, plant available water, reduced bulk density and penetration resistance as compared to the sole applications of PL and inorganic fertilizer.展开更多
文摘With the rapid development of DNA technologies, high throughput genomic data have become a powerful leverage to locate desirable genetic loci associated with traits of importance in various crop species. However, current genetic association mapping analyses are focused on identifying individual QTLs. This study aimed to identify a set of QTLs or genetic markers, which can capture genetic variability for marker-assisted selection. Selecting a set with k loci that can maximize genetic variation out of high throughput genomic data is a challenging issue. In this study, we proposed an adaptive sequential replacement (ASR) method, which is considered a variant of the sequential replacement (SR) method. Through Monte Carlo simulation and comparing with four other selection methods: exhaustive, SR method, forward, and backward methods we found that the ASR method sustains consistent and repeatable results comparable to the exhaustive method with much reduced computational intensity.
文摘Linear mixed model (LMM) approaches have been widely applied in many areas of research data analysis because they offer great flexibility for different data structures and linear model systems. In this study, emphasis is placed on comparing the properties of two LMM approaches: restricted maximum likelihood (REML) and minimum norm quadratic unbiased estimation (MINQUE) with and without resampling techniques being included. Bias, testing power, Type I error, and computing time were compared between REML and MINQUE approaches with and without Jackknife technique based on 500 simulated data sets. Results showed that MINQUE and REML methods performed equally regarding bias, Type I error, and power. Jackknife-based MINQUE and REML greatly improved power compared to non-Jackknife based linear mixed model approaches. Results also showed that MINQUE is more time-saving compared to REML, especially with the use of resampling techniques and large data set analysis. Results from the actual cotton data analysis were in agreement with our simulated results. Therefore, Jackknife-based MINQUE approaches could be recommended to achieve desirable power with reduced time for a large data analysis and model simulations.
文摘Healthy soils are important to ensure satisfactory crop growth and yield. Poultry litter (PL), as an organic fertilizer, has proven to supply the soil with essential macro and micronutrients, enhance soil fertility, and improve crop productivity. Integrating this treatment has the potential to improve soil physical and biological properties by increasing soil carbon, C. However, rapid decomposition and mineralization of PL, particularly in the hot and humid southeastern U.S., resulted in losing C and reduced its effect on soil health. Biochar and lignite have been proposed to stabilize and mitigate C loss through application of fresh manure. However, their combined effects with PL on C sequestration and soil health components are limited. A field experiment was conducted on Leeper silty clay loam soil from 2017 to 2020 to evaluate the combined effect on soil properties when applying biochar and lignite with PL to cotton (Gossypium hirsutum L.). The experimental design was a randomized complete block involving nine treatments replicated three times. Treatments included PL and inorganic nitrogen, N, fertilizer with or without biochar and lignite, and an unfertilized control. Application rates were 6.7 Mgkg⋅ha−1</sup> for PL, 6.7 Mgkg⋅ha−1</sup></sup> for biochar and lignite and 134 kg⋅ha−1</sup><sup></sup> for inorganic N fertilizer. Integration of PL and inorganic fertilizer with biochar and lignite, resulted in greater soil infiltration, aggregate stability, plant available water, reduced bulk density and penetration resistance as compared to the sole applications of PL and inorganic fertilizer.
