Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations. Here we exploited this property to sequence and catalog more than 10 million mutations in the protein-coding regions of 2,735 mutant lines of tetraploid and hexaploid wheat. We detected, on average, 2,705 and 5,351 mutations per tetraploid and hexaploid line, respectively, which resulted in 35-40 mutations per kb in each population. With these mutation densities, we identified an average of 23-24 missense and truncation alleles per gene, with at least one truncation or deleterious missense mutation in more than 90% of the captured wheat genes per population. This public collection of mutant seed stocks and sequence data enables rapid identification of mutations in the different copies of the wheat genes, which can be combined to uncover previously hidden variation. Polyploidy is a central phenomenon in plant evolution, and many crop species have undergone recent genome duplication events. Therefore, the general strategy and methods developed herein can benefit other polyploid crops.wheat | polyploidy | mutations | reverse genetics | exome capture S ince the dawn of agriculture, wheat has been a major dietary source of calories and protein for humans. The cultivated wheat species Triticum turgidum (tetraploid, AABB genome) and Triticum aestivum (hexaploid, AABBDD genome) originated via recent polyploidization events followed by domestication.

It is essential to standardize the definitions and approaches to quantifying various irrigation per formance measures. The ASCE Task Committee on Defining Irrigation Efficiency and Uniformity provides a comprehensive examination of various performance indices such as irrigation efficiency, application efficiency, irrigation sagacity, distribution uniformity, and others. Consistency is provided among different irrigation meth ods and different scales. Clarification of common points of confusion is provided, and methods are proposed whereby the accuracy of numerical values of the performance indicators can be assessed. This issue has two companion papers that provide more detailed information on statistical distribution uniformity and the accuracy of irrigation efficiency estimates.

Discovery of rare mutations in populations requires methods, such as TILLING (for Targeting Induced Local Lesions in Genomes), for processing and analyzing many individuals in parallel. Previous TILLING protocols employed enzymatic or physical discrimination of heteroduplexed from homoduplexed target DNA. Using mutant populations of rice (Oryza sativa) and wheat (Triticum durum), we developed a method based on Illumina sequencing of target genes amplified from multidimensionally pooled templates representing 768 individuals per experiment. Parallel processing of sequencing libraries was aided by unique tracer sequences and barcodes allowing flexibility in the number and pooling arrangement of targeted genes, species, and pooling scheme. Sequencing reads were processed and aligned to the reference to identify possible single-nucleotide changes, which were then evaluated for frequency, sequencing quality, intersection pattern in pools, and statistical relevance to produce a Bayesian score with an associated confidence threshold. Discovery was robust both in rice and wheat using either bidimensional or tridimensional pooling schemes. The method compared favorably with other molecular and computational approaches, providing high sensitivity and specificity.

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Key message Chromosome regions affecting grain yield, grain yield components and plant water status were identified and validated in fall-sown spring wheats grown under full and limited irrigation. AbstractIncreases in wheat production are required to feed a growing human population. To understand the genetic basis of grain yield in fall-sown spring wheats, we performed a genome-wide association study (GWAS) including 262 photoperiod-insensitive spring wheat accessions grown under full and limited irrigation treatments. Analysis of molecular variance showed that 4.1% of the total variation in the panel was partitioned among accessions originally developed under fall-sowing or spring-sowing conditions, 11.7% among breeding programs within sowing times and 84.2% among accessions within breeding programs. We first identified QTL for grain yield, yield components and plant water status that were significant in at least three environments in the GWAS, and then selected those that were also significant in at least two environments in a panel of eight biparental mapping populations. We identified and validated 14 QTL for grain yield, 15 for number of spikelets per spike, one for kernel number per spike, 11 for kernel weight and 9 for water status, which were not associated with differences in plant height or heading date. We detected significant correlations among traits and colocated QTL that were consistent with those correlations. Among those, grain yield and plant water status were negatively correlated in all environments, and six QTL for these traits were colocated or tightly linked (< 1 cM). QTL identified and validated in this study provide useful information for the improvement of fall-sown spring wheats under full and limited irrigation.Electronic supplementary materialThe online version of this article (10.1007/s00122-018-3111-9) contains supplementary material, which is available to authorized users.

The Priestley-Taylor (PT) approximation for computing evapotranspiration was initially developed for conditions of a horizontally uniform saturated surface sufficiently extended to obviate any significant advection of energy. Nevertheless, the PT approach has been effectively implemented within the framework of a thermal-based two-source model (TSM) of the surface energy balance, yielding reasonable latent heat flux estimates over a range in vegetative cover and climate conditions. In the TSM, however, the PT approach is applied only to the canopy component of the latent heat flux, which may behave more conservatively than the bulk (soil 1 canopy) system. The objective of this research is to investigate the response of the canopy and bulk PT parameters to varying leaf area index (LAI) and vapor pressure deficit (VPD) in both natural and agricultural vegetated systems, to better understand the utility and limitations of this approximation within the context of the TSM. Micrometeorological flux measurements collected at multiple sites under a wide range of atmospheric conditions were used to implement an optimization scheme, assessing the value of the PT parameter for best performance of the TSM. Overall, the findings suggest that within the context of the TSM, the optimal canopy PT coefficient for agricultural crops appears to have a fairly conservative value of ;1.2 except when under very high vapor pressure deficit (VPD) conditions, when its value increases. For natural vegetation (primarily grasslands), the optimal canopy PT coefficient assumed lower values on average (;0.9) and dropped even further at high values of VPD. This analysis provides some insight as to why the PT approach, initially developed for regional estimates of potential evapotranspiration, can be used successfully in the TSM scheme to yield reliable heat flux estimates over a variety of land cover types.

Photosynthetically active radiation (PAR) is a necessary input in several crop growth models. Previous research from several locations with different instruments has suggested that PAR could be estimated as a constant fraction of shortwave radiation. This study was conducted to determine if a simple relationship was valid for a large geographic area in the western half of the USA. In the semiarid climate near Fresno, CA, the daily photosynthetic photon flux density (PPFD) in units of μmol m−2 was 2.04 ± 0.06 times the solar irradiance (SI). The daily irradiance within the PAR waveband (photosynthetic irradiance (PI), 0.4 to 0.7 μm) was estimated to be 45% of the daily solar irradiance. The diurnal pattern of these relationships was consistent with measurements at Phoenix, AZ and exhibited only a slight diurnal variation. Independent measurements of the solar irradiance between 0.285 and 0.63 μm with “filtered” pyranometers at the Fresno site indicated that irradiance between 0.285 and 0.63 μm was 41% of solar irradiance, a result which was about 7% lower than the estimate from the PAR/SI value converted with a published sun and sky PAR/PI factor. This difference was largely attributed to the differences in measured wavebands. Measurements of solar irradiance less than the waveband of 0.63 μm and total solar irradiance obtained with the same equipment at Brawley, CA; Weslaco, TX; Temple, TX; Manhattan, KS; Lincoln, NE; St. Paul, MN; Fargo, ND; Sidney, MT; Beartooth Pass, WY; Kimberly, ID; Davis, CA were similar to those measured at Fresno, CA. The results indicate that PAR can be estimated from solar irradiance measurements to within 10% (which is probably acceptable for most plant growth models) throughout most of the Western USA.

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