This study provides supplemental data to support the study on Optimizing Genomic-Enabled Prediction: A Feature Weighting Approach for Enhancing within Family Accuracy.
Interspecific hybrids can be formed through allopolyploidization. Synthetic hexaploid wheats (SHW) have been created in breeding programs through the intentional crossing of tetraploid and diploid species. In this study, quantitative genetics tools developed to predict cross performance within a species were applied to predict the phenotypes of SHW for four major quantitatively inherited diseases using the data contained in this dataset. The results of the analysis are presented in the accompanying article.
Maize stalk rot can cause significant economic losses for maize farmers around the world. Information on the genetic architecture of maize stalk rot could help breeders design effective breeding strategies to enhance resistance to stalk rot. This dataset was used to carry out genome-wide association analysis (GWAS) and genomic prediction for stalk rot in mid-altitude tropical maize populations. It includes phenotypic data from testcross hybrids of 677 inbred lines from the Tuxpeño and non-Tuxpeño heterotic pools evaluated in three environments. Genotypic data for 200,681 single nucleotide polymorphisms (SNPs) used for GWAS and genomic prediction are also provided. The results of the analyses are described in the accompanying article.
Lower yield of wheat in eastern India can be attributed to several input factors i.e., inappropriate crop management practices including other social and environmental factors. Among them, sub-optimal irrigation is one of the important factors. Recommended number of irrigations for optimal wheat harvest is 4-5 depending upon crop growth stages and availability of water. Observations by the project team and a recent survey conducted by CSISA at a landscape-level found that majority of farmers in this part of India apply 2-3 irrigations. Moreover, several studies have suggested to apply irrigation to wheat at its grain filling stage to protect the crop from terminal heat stress thereby safeguarding yield. To validate the effect of number of irrigations and irrigation at the grain-filling stage of wheat, multi-location on-farm trials were conducted continuously over six years starting from 2016-17. Krishi Vigyan Kendras, district-level extension center of national agriculture research and extension system were involved in this process. Ten districts were selected in a way that all agro-climatic zones of this area are covered. The treatment in this trial was application of additional irrigation at maturity/grain-filling stage of wheat crop against general farmer practice. Number of irrigations with farmers vary from 1 to 4, so our treatments included 1+1, 2+1, 3+1, and 4+1 irrigations. We applied these treatments in two sets of wheat crop establishment i.e., zero-tillage and conventional tillage methods. There is asymmetry in distribution of samples within treatments and over years. That happened as trial was in farmer’s participatory mode and numbers were dependent completely on willingness of farmers to participate. Altogether, the trial was conducted at 1810 sites, and we captured 63 variables including yield and yield attributing traits.
CIMMYT annually distributes improved germplasm developed by its researchers and partners in international nurseries trials and experiments. The High Temperature Wheat Yield Trial (HTWYT) is a replicated yield trial that contains spring bread wheat (Triticum aestivum) germplasm adapted to Mega-environment 1 (ME1) which represents high temperature areas.
CIMMYT annually distributes improved germplasm developed by its researchers and partners in international nurseries trials and experiments. The High Rainfall Wheat Yield Trial (HRWYT) contains very top-yielding advance lines of spring bread wheat (Triticum aestivum) germplasm adapted to high rainfall, Wheat Mega-environment 2 (ME2HR).
Two types of experiments conducted in multi-location on-farm trials to evaluate the mechanized crop establishment methods (Drill-Direct Seeded Rice and Mechanical Transplanted Rice) alternative to traditional crop establishment methods (Manual transplanted rice and broadcasting followed by beushening) in three districts of Odisha over three years (2017 to 2019). Two types of experiments were also conducted to evaluated the performance of short duration pulses or oilseeds in the rice-fallow areas for increasing the cropping intensity and system productivity. The yield data were collected manually from different treatments under each experiment over three years. We also combined multi-temporal Earth Observation (EO) data from Landsat-8 Operational Land Imager (OLI) and Sentinel-1 satellite sensors from 2018 to 2021 to identify rice-fallow areas and suitable rice-fallow areas for cultivation of short duration pulses and oilseeds.
Low soil nitrogen stress can contribute to food insecurity, malnutrition, and rural poverty in maize-dependent smallholder communities of sub-Saharan Africa (SSA). Enhanced selection for improved varieites may result from a better understanding of the genomic regions associated with low nitrogen tolerance. Four F3 maize populations were used to study the genetic architecture of grain yield (GY) and its associated traits (anthesis-silking interval (ASI), anthesis date (AD), plant height (PH), ear position (EPO), and ear height (EH)) under different soil nitrogen regimes in Kenya and Zimbabwe. Information about the populations and the genotypic data used in the analyses are provided in this dataset. The results of the analysis are reported in the related journal article.
The Elite Spring Wheat Yield Trial (ESWYT) is a replicated yield trial that contains spring bread wheat (Triticum aestivum) germplasm adapted to Mega-environment 1 (ME1) which represents the optimally irrigated, low rainfall areas. Major stresses include leaf, stem and yellow rusts, Karnal bunt, and lodging. Representative areas include the Gangetic Valley (India), the Indus Valley (Pakistan), the Nile Valley (Egypt), irrigated river valleys in parts of China (e.g. Chengdu), and the Yaqui Valley (Mexico). This ME encompasses 36 million hectares spread primarily over Asia and Africa between 350S -350N latitudes. White (amber)-grained types are preferred by consumers of wheat in the vast majority of the areas. It is distributed to upto 200 locations and contains 50 entries.
Maydis Leaf Blight (MLB) is a serious foliar disease for maize in warm and humid regions. The data in this dataset were used to investigate the genetic architecture underlying resistance to MLB using high resolution Genome Wide Association Studies and Genomic Prediction. A diverse panel of 336 maize inbreds adapted for the Asian tropics, were evaluated for MLB disease score under four environments using artificial inoculation. In addition, a set of high density SNPs (128,490) from genotyping by sequencing were used for the study. The results of this study are presented in the accompanying publication.