Subsets Of Varieties Research Articles

An investigation of the impact of imbalance on the analysis of the US crop variety evaluation program data

AbstractMulti‐environment trial data from many crop variety evaluation programs are imbalanced because only a subset of varieties is selected for the following year, which leads to missing variety by year. Inspired by the US National Cotton Variety Test trial, we conducted new simulation studies to investigate selection processes that differ from the existing literature. The followings are our four main contributions. First, we adopted a framework that utilizes a logistic regression to generate imbalanced data that follow missing completely at random, missing at random, or missing not at random (MNAR). Second, our selection process can depend on multiple traits, whereas all existing studies only used a single trait for selection. Third, besides variance components (VCs), long‐term trends that reflect genetic and non‐genetic development are of interest since the simulated data span over 30 years. Last, we evaluated the prediction accuracy for variety's overall and location‐specific performance. The results show that the VC and long‐term trends estimations are the worst under MNAR using the single trait for selection. Compared to VC, the long‐term trends estimation is more influenced by the missing mechanism and missing rate. However, the prediction accuracy for variety's performance is mainly driven by the missing rate and is less sensitive to the selection process. If ignoring the genetic and non‐genetic long‐term trends, both estimation and prediction will deteriorate. More testing years would improve estimation and prediction, despite a higher missing rate.

β-diketone accumulation in response to drought stress is weakened in modern bread wheat varieties (Triticum aestivum L.).

Cuticular waxes coating leaf surfaces can help plants tolerate drought events by reducing non-stomatal water loss. Despite their role in drought tolerance, little is known about how cuticular wax composition has changed during breeding in Canadian bread wheat (Triticum aestivum L.) varieties. To fill in this gap, flag leaves of the Canadian Heritage Bread Wheat Panel, which include 30 varieties released between 1842 and 2018, were surveyed to determine if and how cuticular wax composition in wheat has changed at two breeding ecozones over this period. Following this, a subset of varieties was subjected to drought conditions to compare their responses. As expected, modern varieties outperformed old varieties with a significantly larger head length and reaching maturity earlier. Yet, when challenged with drought, old varieties were able to significantly increase the accumulation of β-diketones to a higher extent than modern varieties. Furthermore, RNAseq was performed on the flag leaf of four modern varieties to identify potential markers that could be used for selection of higher accumulation of cuticular waxes. This analysis revealed that the W1 locus is a good candidate for selecting higher accumulation of β-diketones. These findings indicate that the variation in cuticular waxes upon drought could be further incorporated in breeding of future bread wheat varieties.

Naked oats: metabolisable energy yield from a range of varieties in broilers, cockerels and turkeys

1. Naked oats belong to the same species as ‘common oats’, Avena sativa, but have a non-lignified husk which readily becomes detached during harvesting. The absence of the indigestible husk can be predicted to give an increased metabolisable energy (ME) content for poultry. 2. Measurements of true metabolisable energy (TMEN) were performed on 3-week-old broiler chicks (Cobb males), adult cockerels (ISA Brown, greater than one year old) and 7-week-old turkeys (BUT T8 males). The measurements were repeated in 2000, 2001 and 2002, with some measurements on a subset of varieties in 2004. 3. High-oil naked oat lines yielded 12% more energy (TMEN) than wheat. Naked oats, excluding the experimental high-oil lines, yielded 8·5% more energy than simultaneously assayed wheat samples. 4. In samples from the 2004 harvest, conventional oats gave TMEN values about 13% lower than those of wheat. 5. The addition of β-glucanase produced an increase of about 4% in the apparent metabolisable energy (AME) of oats for broiler chickens. This effect was associated with a 70% decrease in the jejunal viscosity of broilers receiving a 500 g/kg naked-oat diet. 6. The oil content of naked oats was about 5 times greater than that of wheat, with the high-oil lines rising to more than 6 times greater. Naked oats had a lower starch content than wheat but not sufficiently lower to negate the energy benefits of the higher oil content. The crude protein (CP) contents of naked oats were similar to those of wheat, with the high-oil varieties tending to be higher in CP also.

Identification of barley and rye varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks.

Cereal varieties are normally identified using time-consuming methods such as visual examination of either the intact grain or one-dimensional electrophoretic patterns of the grain storage proteins. A fast method for identification of wheat (Triticum aestivum L.) varieties has previously been developed, which combines analysis of alcohol-soluble wheat proteins (gliadins) using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks. Here we have applied the same method for the identification of both barley (Hordeum vulgare L.) and rye (Secale cereale L.) varieties. For barley, 95% of the mass spectra were correctly classified. This is an encouraging result, since in earlier experiments only a grouping into subsets of varieties was possible. However, the method was not useful in the classification of rye, due to the strong similarity between mass spectra of different varieties.

Differential Tolerance of Corn (Zea mays) Inbreds to Four Sulfonylurea Herbicides and Bentazon

Nine corn inbreds were selected from a test on 250 inbreds based on distinctly different response to herbicides. These inbreds showed up to 50,000-fold differences, which varied by inbred and herbicide. Only the inbred GA209 was sensitive to bentazon and the four sulfonylurea herbicides. GA209 and B90 were the most sensitive inbreds to the sulfonylurea herbicides. F2R was generally the most tolerant inbred. The pattern of herbicide tolerance varied greatly. For example, the relative tolerance of F2 to thifensulfuron was 12-fold more than to rimsulfuron while Mo17 was 56-fold more tolerant to rimsulfuron than thifensulfuron. F2 was fivefold more tolerant of chlorsulfuron than chlorimuron, whereas B80 was 100-fold the reverse. These inbreds provide a small subset of varieties to evaluate the large and inherent differences in herbicide tolerance of corn.

A comparison of results obtained with two methods for assessing yield stability

A major objective of the CIMMYT Maize Program is to develop open-pollinated varieties of maize (Zea mays L.) that are well adapted to a wide range of environments. To achieve this breeding goal, it is essential that the program use a stability technique that will identify high-yielding, stable genotypes accurately in international trials conducted under different environmental conditions. The objective of this study was to compare a spatial method with a modified conventional regression analysis method to determine the yield stability of 27 CIMMYT maize varieties evaluated at 37 locations. The methods also were compared on the basis of their consistency in assessing the stability of varieties when certain locations were omitted, and when subsets of varieties were analyzed. The varieties found to be stable by the spatial method with all sites included in the analysis were also stable (1) when the lowest and highest yielding sites were excluded from the analyses, and (2) when the varieties were considered, along with others, as a subset of the original group of materials. Stability parameters determined by regression analysis, however, varied for some varieties when (1) extreme sites were excluded, and (2) a subset of entries was considered in isolation. Because the spatial method was more consistent in identifying high-yielding stable varieties, it was considered the more useful of the two methods.