Genetic and environmental analysis of NIR feed quality predictions on genotypes of barley (Hordeum vulgare L.)

This study investigated the use of NIR feed quality equations, developed from a multi-cereal calibration set, including barley, on barley breeding lines and commercial cultivars. The resultant predictions were then analysed to ascertain genetic and or environmental affects. The calibrations were developed by a third party, using a NIRSystems 6500 (master) instrument. The barley spectra we used were also from the same model of instrument, which had been spectrally standardised to match the master instrument. The breeding lines and commercial cultivars used were obtained from a field trial series which combined intermediate and advanced breeding lines, grown at 11 environments over two seasons. The results indicated there were significant (P < 0.05) genetic and environmental effects on a broad range of feed quality related traits; including metabolisible energy, digestible energy and apparent metabolisible energy. Other feed traits such as acid detergent fibre, neutral detergent fibre, β-glucan and starch also showed significant (P < 0.05) genetic and environmental affects. There was a high level of heritability for most traits, ranging from 70 to 90%. The results identified a number of strongly correlated traits when analysed by factor analysis. These included starch and the energy traits. There were no strong associations between particular cultivars and the NIR predicted feed traits. The results from this study highlighted NIR equations for predicted feed quality that can provide data to assist selection of barley breeding lines. In addition, the analysis also showed the genetic and environmental effects that could be expected to be observed in a broad range of barley breeding material and commercial varieties. This information can be combined in breeding programs to identify robust barley lines that would be suited to specific animal feed classes.     

Apigenin di-C-glycosides (ACG) content and composition in grains of bread wheat (Triticum aestivum) and related species

Apigenin di-C-glycosides (ACGs) are present in the grain of bread wheat and other related cereals primarily as one or two sets of Wesseley-Moser isomers containing either arabinose and glucose (ACG1) or arabinose and galactose (ACG2) on the A ring of apigenin. These compounds may contribute to the yellow colour of wheat-based products made under alkaline conditions and in addition, have possible roles in a number of plant physiology processes and human health. The aims of this investigation were to survey genetic variation for ACG content and composition in hexaploid bread wheat (Triticum aestivum L.) and to examine ACGs in the putative progenitors of hexaploid wheat and available genetic stocks as a first step towards understanding the mechanisms involved in their biosynthesis and genetic control. Substantial variation in both grain ACG content and the ratio, ACG1/ACG2, were identified within bread wheat cultivars and related species. Genotype controlled the major portion of the variation. ACG content appeared to be a multigenic trait whereas variation in ACG1/ACG2 was associated with a limited number of chromosomes, in particular chromosomes 1B, 7B and 7D. The results suggest that it should be possible to manipulate both ACG content and composition traits through breeding.     

大麦穗长和株高QTL的鉴定

为挖掘大麦穗长和株高的QTL位点,以1个大麦重组自交系（recombinant inbred line,RIL）群体（以J36528和BMJ89为亲本,包含125个F₁₀代）为材料,基于本课题组前期利用DArT标记构建的连锁图谱,结合4年2点共6个不同生态环境测得的穗长和株高表型数据,鉴定大麦穗长和株高QTL。结果表明,共鉴定到3个穗长QTL和2个株高QTL,分别分布在2H、3H、6H和7H染色体上,其中,穗长位点 Qsl.sicau-JB-2H在2个环境中被检测到,能够解释11.38%~14.66%的表型变异; Qsl.sicau-JB-7H在6个环境中均被检测到,能够解释35.10%~46.34%的表型变异;而 Qph.sicau-JB-6H仅在1个环境中被检测到,可解释17.99%的表型变异。株高位点 Qph.sicau-JB-6H在5个环境中均被检测到,能够解释16.36%~21.18%的表型变异;而 Qph.sicau-JB-3H仅在1个环境中被检测到,可解释15.40%的表型变异。本研究为解析大麦植株形态和产量性状遗传机制以及分子辅助育种奠定了基础。     

The potential contribution of wild barley (Hordeum vulgare ssp. spontaneum) germplasm to drought tolerance of cultivated barley (H. vulgare ssp. vulgare)

Improving drought tolerance has always been an important objective in many crop improvement programs and is becoming more important as one way of adapting crops to climate changes. However, due to its complexity, the genetic mechanisms underlying the expression of drought tolerance in plants are poorly understood and this trait is difficult to characterize and quantify. This study assessed the importance of the wild progenitor of cultivated barley, Hordeum spontaneum C. Koch, in contributing developmental and yield-related traits associated with drought tolerance and therefore its usefulness in breeding for improved adaptation to drought stress conditions. Fifty-seven fixed barley lines derived from crosses with two H. spontaneum lines (41-1 and 41-5) were evaluated in Mediterranean low rainfall environments with 10 improved varieties and three landraces for grain yield, developmental and agronomic traits. The study was conducted for three years (2004–2006) in a total of nine environments (location–year combinations), eight in Syria and one in Jordan, which were eventually reduced to seven due to a large error variance in two of them. There was significant genetic variation among the genotypes for most of the traits measured, as well as differential responses of genotypes across environments. Traits such as peduncle length, peduncle extrusion and plant height were positively correlated with grain yield in the dry environments. Differences in phenology were small and not significantly correlated with differences in grain yield under stress. Performances at the three highest yielding environments were much more closely correlated than those at the four stress environments. The GGE biplot analysis allowed identification of genotypes consistently best adapted to the lowest yielding environments and confirmed the existence of unique environments for identifying better adapted genotypes in the low rainfall environments of Syria. The top yielding lines in the driest of the seven environments derived mostly from crosses with H. spontaneum 41-1, while most of the improved varieties showed a positive genotype by environment (GE) interaction with the highest yielding environments. The results of the field experiments indicated that there was variation for grain yield under drought stress among barley genotypes, and that some of the lines derived from H. spontaneum had consistently superior specific adaptation to the range of severe stress conditions used in this study. The usefulness of H. spontaneum in breeding programs for stress conditions is likely to increase in view of the predicted increase in the occurrence of high temperatures and droughts.     

Barley for food: Characteristics,improvement, and renewed interest

Barley (Hordeum vulgare vulgare L.) is an ancient cereal grain, which upon domestication has evolved from largely a food grain to a feed and malting grain. However, barley food use today remains important in some cultures around the world, particularly in Asia and northern Africa, and there is renewed interest throughout the world in barley food because of its nutritional value. This review covers basic and general information on barley food use and barley grain processing for food use, as well as an in-depth look at several major aspects/traits of interest for barley food use including kernel hardness and colour, grain starch, and β-glucan contents. These traits are described in terms of their effects on processing and nutrition, as well as their inheritance and the prospects for barley improvement through breeding. Whereas, the aspects listed above have been studied relatively extensively in barley in terms of content, form, genetics, physiology, and in some cases nutritional quality, little is know about functional properties for processing and food product development. Renewed interest in barley for food uses largely centres around the effects of β-glucans on lowering blood cholesterol levels and glycemic index. Wholegrain barley foods also appear to be associated with increased satiety and weight loss. There is great potential to utilise barley in a large number of cereal-based food products as a substitute partially or wholly for currently used cereal grains such as wheat (Triticum aestivum), oat (Avena sativa), rice (Oryza sativa), and maize (Zea mays).     

QTL mapping for crude protein and protein fraction contents in rice (Oryza sativa L.)

Improvement of rice storage proteins is important in rice breeding for high nutritional quality. Seventy-one recombinant inbred lines (RIL) derived from a cross between japonica variety Asominori and indica variety IR24 were used to study the inheritance of crude protein and protein fraction contents in rice. A total of 16 QTL were identified and mapped on eight chromosomes. Several QTL affecting contents of different protein fractions were mapped in the same chromosomal region. In particular, two QTL with a significant contribution were identified to simultaneously affect prolamin and glutelin contents. One QTL denoted as qCP-12 affecting crude protein content (CP) was located in the same region as QTL qGLT-12 affecting glutelin content, in agreement with the positive correlation between glutelin level and protein content. QTL with larger genetic effects were further confirmed using two sets of chromosome segment substitution lines (CSSL), where Asominori and IR24 were used as the recurrent parents. By QTL comparative analysis, two QTL for CP, three for globulin content and one for prolamin content were located in the vicinity of CP QTL previously identified in polished rice. Application of these results in rice breeding is discussed.     

Barley (1→3; 1→4)-β-glucan and arabinoxylan content are related to kernel hardness and water uptake

Harder kernels in barley are thought to be a factor affecting the modification of the endosperm during malting by restricting water and enzyme movement within the endosperm. The objective of this study was to investigate the relationship between kernel hardness, water uptake and the endosperm composition in barley. A range of barley samples from 2003 and 2004 crops were analyzed for kernel hardness by the Single Kernel Characterization System, water uptake during steeping and chemical composition of the endosperm including (1→3; 1→4)-β-glucan, arabinoxylan and total protein. Both (1→3; 1→4)-β-glucan and arabinoxylan content of the endosperm were correlated significantly with kernel hardness in barley samples from both 2003 (r=0.873 and 0.601, respectively, p<0.01) and 2004 seasons (r=0.764 and 0.501, respectively, p<0.01). Hardness of the kernel was highly correlated with its water uptake in both 2003 and 2004 samples (r=−0.853 and −0.752, respectively, p<0.01). β-Glucan content of the endosperm was also correlated significantly with the kernel water uptake for both years (2003: r=−0.752, p<0.01; 2004: r=−0.551, p<0.01). Arabinoxylan content of the endosperm was correlated significantly with the kernel water uptake for the 2003 barley but not for 2004 barley (2003: r=−0.523, p<0.01; 2004: r=−0.151, p>0.01). Protein content of the endosperm was not correlated with the kernel hardness in either year. These results demonstrate that endosperm cell wall components may have significant impact on kernel hardness as well as water uptake of barley.     

Molecular analyses of genetic variability in soap nut (Sapindus mukorossi Gaertn.)

Sapindus mukorossi Gaertn. (Sapindaceae) is commercially an important plant much valued for its fruits commonly known as soap nut as well as for the seed oil used as a feed-stock for biodiesel production. Molecular polymorphism, determined, using three single primer amplification reaction (SPAR) methods (RAPD, DAMD and ISSR) is used to assess the genetic variability in 69 accessions of S. mukorossi Gaertn., encompassing different geographical regions in India. Cumulative band data generated using the three SPAR methods resulted in 82.49% polymorphism across all genotypes of S. mukorossi Gaertn. UPGMA tree showed two major clusters that were in accordance with the geographical diversity. The intra-population genetic diversity (0.16), Shannon information index (0.24) and polymorphic loci (45.62%) were highest in AS population, while the corresponding lowest values were recorded in HP population. The inter-population average distance ranged from 0.05 (GA and HP) to 0.26 (AP and HP). Based on these distances, the UPGMA tree for the populations was computed, which showed the presence of two major clusters. Cluster I contained all the populations from Himachal Pradesh (HP) and Uttarakhand (GA and KU) and cluster II grouped the populations from North Eastern region (AS, AP, MG). The present study showed that SPAR methods are informative and useful to unravel the diversity among different populations of the soap nut plants and is a prelude for further utilization of promising and genetically divergent materials in the breeding programmes.     

Molecular genetic mapping of NIR spectra variation

A novel analytical approach was used to identify associations between Near-Infrared (NIR) spectral fingerprints and segments of wheat (Triticum aestivum L.) chromosomes indicating the location of genetic factors contributing to variation in NIR spectra. To identify the genetic factors, environmental and experimental variability were removed from the spectra using spatial mixed models. These corrected spectra were combined with the molecular genetic analysis of wheat lines from a structured population derived from a Carnamah by WAWHT2046 doubled haploid set of progeny. The association of chromosome segments with specific NIR wavelengths was established using all-subset regression and canonical correlation methodology. These improved processes for analysing NIR spectra were validated using 161 lines in breeding trials analysed over a period of 3 years across 40 sites.     

Prediction of total phenols,condensed tannins,and 3-deoxyanthocyanidins in sorghum grain using near-infrared (NIR) spectroscopy

The reported high phenolic levels in sorghum have led an interest from sorghum breeding programs in developing and identifying germplasms with high phenolic levels, which require screening a large number of samples to find those with the highest levels. Since wet chemistry screening methods are slow, expensive, and destructive, the use of NIR calibration curves could be an alternative. The objectives of this project were to determine the variation range in total phenols, condensed tannins, and 3-deoxyanthocyanidin levels in a diverse set of sorghum genotypes and to assess the predictive value of NIR curves to estimate these compounds in sorghum. A calibration curve to estimate each compound was developed and validated with an independent validation set. Calibration curve correlations for total phenols, condensed tannins, and 3-deoxyanthocyanidins were r = 0.98, 0.97, and 0.99, respectively. Correlations between NIR-predicted values and reference values in the validation set were significant for total phenols (r = 0.93), condensed tannins (r = 0.81) and 3-deoxyanthocyanidin (r = 0.82). These indicated that sufficient variation for these compounds existed within sorghum and that NIR calibration curves could be used to rapidly and non-destructively predict total phenols, condensed tannins, and 3-deoxyanthocyanidins concentrations in whole grain sorghum.     

Genetics of intra-gene pool and inter-gene pool hybridization for seed traits in common bean (Phaseolus vulgaris L.) germplasm from Europe

Due to adaptation to new ecological and manmade conditions, the large diversity evolved in the European common bean germplasm is of particular interest for plant breeding. The knowledge of the genetic relationships within and among races and gene pools and their performance per se will provide bean breeders with a starting point in designing crosses using contrasting and complementary parents to broaden the genetic base within the different commercial classes. A genetic study of seed size variation and protein markers in progeny derived from 16 intraracial, interracial and inter-gene pools European common bean populations was conducted. General and specific combining ability (GCA and SCA) values were significant for seed weight, indicating that both additive and nonadditive genetic effects were involved in conditioning seed weight. Interracial populations showed transgressive values due to the accumulation of large-seeded alleles. Genetic variation inside Andean germplasm, and Chile and Peru races in particular, exhibited useful genetic progress in these populations, providing lines with a large seed size, and so, an excellent market potential. The distribution of incompatibility between both gene pools (Mesoamerican and Andean) of the common bean was explored. Inter-gene pool populations provided lower means of inbred segregants than the mid-parent value. Therefore, a good option it would be select for large seed size according to a recurrent or congruity inbred-backcrossing selection programs. Analysis of allele markers frequencies in inter-gene populations showed segregation distortion with a higher than expected frequency of alleles from the Mesoamerican gene pool, many of which were fixed in the F₇ lines. The presence of a great percentage of markers that showed segregation distortion in these populations (87%) indicated that this phenomenon can be amplified by using distance related common bean genotypes. In addition, a high percentage of heterozygotes for the Phs locus (for the seed storage protein phaseolin) was found, which suggest that the Andean homozygous TT could not be expressed in Mesoamerican genetic background due to the action of some form of female specific mechanisms that affected gene exchange between parental germplasm in inter-gene pool populations. The present work provides useful information in the establishment of large seed size germplasm that could have a great deal of interest among breeders and may offer some possibilities to exploit existing variation within and between common bean races.     

A chemometric evaluation of the underlying physical and chemical patterns that support near infrared spectroscopy of barley seeds as a tool for explorative classification of endosperm genes and gene combinations

Near infrared spectroscopic (NIR; 1100–2500 nm), chemical and genetic data were combined to study the pleiotropic secondary effects of mutant genes on milled samples in a barley seed model. NIR and chemical data were both effective in classifying gene and gene combinations by Principal Component Analysis (PCA). Risø mutants R-13, R-29 high (1→3, 1→4)-β-glucan, low starch and R-1508 (high lysine, reduced starch), near isogeneic controls and normal lines and recombinants were studied. Based on proteome analysis results, six anti-microbial proteins were followed during endosperm development revealing pleiotropic gene effects in expression timing that supporting the gene classification. To verify that NIR spectroscopy data represents a physio–chemical fingerprint of the barley seed, physical and chemical spectral components were partially separated by Multiple Scatter Correction and their genetic classification ability verified. Wavelength bands with known water binding and (1→3, 1→4)-β-glucan assignments were successfully predicted by partial least squares regression giving insight into how NIR-data works in classification. Highly reproducible gene-specific, covariate, pleiotropic classification patterns from NIR and chemical data were demonstrated in PCAs and by visual inspection of NIR spectra. Thus PCA classification of NIR-data gives the classical genetic concept, ‘pleiotropy’, a new operational definition as a fingerprint from a spectroscopic representation of the phenome carrying genetic, physical and chemical information. It is concluded that barley seed phenotyping by NIR and chemometrics is a new, reliable tool for characterising the pleiotropic effects of mutant gene combinations and other genotypes in selecting barley for quality in plant breeding.     

小麦三个品质性状微量检测方法的应用与评价

为探讨小麦育种中简单、可行和高效的品质选择指标,给小麦品质改良提供借鉴,对蛋白质含量、籽粒硬度和SDS沉淀值在本单位育种中的应用效果进行分析,结果表明籽粒硬度在不同基因型间的变异系数最大,在不同栽培条件和不同年份表现稳定,是有效、可靠的选择指标;SDS沉淀值与蛋白质含量、籽粒硬度均呈极显著正相关,在基因型间的变异较大,可作为一个能反映总体品质水平的选择指标;蛋白质含量在基因型间变异系数小,受环境影响大,用于早代选择效果不理想。品质育种中可根据籽粒硬度和SDS沉淀值进行初步选择。     

普通小麦籽粒硬度的全基因组关联分析

籽粒硬度是小麦品质评价的重要指标。为挖掘控制小麦籽粒硬度的重要基因/位点,以国内外171个小麦品种组成的自然群体为材料,在4个环境下利用小麦90K SNP芯片对籽粒硬度进行全基因组关联分析(genome-wide association study, GWAS)。171个小麦品种籽粒硬度变异系数为56.59%～66.80%,相关系数为0.88～0.92。GWAS结果表明,共检测到20个与小麦籽粒硬度显著相关的SNPs,其中,14个SNPs(7个位点)在2个及以上环境中能被检测到,分别位于1A、1B、1D、2A、5A和7A染色体上,可解释6.76%～11.79%的表型变异。表型贡献率超过10%的SNPs有4个(3个位点),分布在1D、2A和5A染色体上,其中,1D染色体上的标记wsnp_Ku_c19622_29138795在3个环境中能被检测到,可解释9.08%～11.79%的表型变异;2A染色体上的标记Excalibur_c12675_1789在4个环境中均能被检测到,可解释9.10%～10.86%的表型变异;5A染色体上的标记wsnp_Ra_c24707_34262900和BS00041219_51在2个环境中能被检测到,可解释6.76%～10.35%的表型变异。在所有环境下均与小麦籽粒硬度显著相关的位点有4个,分别位于1A、1B、2A和7A染色体上。     

Calibration of near infrared reflectance spectroscopy to estimate nitrogen concentration in potato tissues

Summary Calibrations are provided to relate near infrared reflectance (NIR) data to total N concentration in potato leaves, stems, and tubers, estimated by Dumas combustion. Separate calibrations are necessary for each tissue-type. the NIR models simulate Dumas [N] estimates accurately, quickly and cheaply and have been shown to be stable. The methods of deriving the calibrations, correcting them and then providing independent tests are described.     

大麦籽粒抗性淀粉含量快速测定方法研究

为探索快速高效测定大麦籽粒中抗性淀粉含量的方法，利用衰减全反射中红外（attenuated total reflection mid-infrared spectroscopy,ATR-MIR）和近红外（near-infrared spectroscopy,NIR）光谱技术，分别用3种不同方法进行预处理，建立大麦样品的抗性淀粉含量快速测定红外模型，通过不同预处理预测模型的校正和内部交叉验证结果的比较，依据决定系数（r）和均方根误差（RMSE）筛选出基于ATR-MIR和NIR光谱的最佳预测模型，再对最佳预测模型进行外部验证。结果表明，经基线位移校正+范围归一化（BOC+RN）预处理后的PLS模型为最佳ATR-MIR预测模型；经标准正态变换+Savitzky-Golay法一阶求导（SNV+1thD）的预处理模型为最佳NIR预测模型。用验证集材料对BOC+RN和SNV+1thD最佳预测模型的预测效果进行外部验证，光谱预测值与化学测定值之间没有显著差异，说明两种方法均可以用于大麦籽粒抗性淀粉含量测定；ATR-MIR光谱比NIR光谱具有更好的预测能力。     

Identification of quantitative trait loci for β-glucan concentration in barley grain

The amount of (1 → 3),(1 → 4)-β-d glucan (β-glucan) accumulated in cell walls of barley (Hordeum vulgare L.) kernel is an important determinant for grain end-use. Grain β-glucan concentration is affected by environmental and genetic factors and usually varies from 3 to 6%. In this study, we have analyzed the β-glucan trait in a doubled-haploid (DH) population of 170 lines grown in three separate field trials. Most of the DH lines showed β-glucan values that ranged from that of the low β-glucan parent (cultivar CDC Bold; 3.3%) to that of the high β-glucan parent (breeding line TR251; 5.4%). Eighty-eight lines of the DH population were genotyped using simple sequence repeat (SSR), amplified fragment length polymorphism (AFLP) and diversity array technology (DArT) markers, which were subsequently integrated into a barley genetic map spanning 1059 cM. Interval mapping and multiple-QTL-mapping (MQM) of quantitative trait loci (QTL) from the three trials indicated seven genomic regions associated with low grain β-glucan concentration. For all putative QTLs, the low β-glucan concentration was contributed by alleles from CDC Bold except for two loci on chromosomes 5H that were derived from TR251. A major QTL located to the centromere region of chromosome 7H was identified by both mapping methods for all three trials. The 7H QTL explained up to 39% of the β-glucan concentration and genetic markers associated with the locus may be used to aid selection of high and low β-glucan barley lines.     

西藏部分青稞主要农艺性状分析

为发掘可提供西藏青稞育种利用的优异品种资源，并为西藏青稞生产提供相应的高产栽培技术，考察了来自6个地区34份青稞的主要农艺性状，结果表明，西藏青稞农艺性状存在丰富的遗传变异，具有矮秆、穗数多和千粒重偏低等特点。相关分析表明西藏青稞各农艺性状间存在复杂的相关性，如穗粒数与株高、单株有效穗数与穗长、总小穗与穗长等呈显著或极显著的正相关和偏相关，单株有效穗数与株高呈极显著的负相关，千粒重与单株有效穗数呈极显著的负偏相关。主成分分析将西藏部分青稞7个农艺性状分为4个主成分，其累积贡献率为91.192%，穗型的贡献率最高，达到46.4338%。供试材料在遗传距离5.18水平上可聚为三大类，分为矮秆短穗少粒型、长穗多粒型、穗多粒重型等三种类型。     

西藏部分青稞主要农艺性状分析

为发掘西藏青稞的优异种质资源,考察了来自西藏6个地区34份青稞的主要农艺性状。结果表明,西藏青稞农艺性状存在丰富的遗传变异,具有矮秆、穗数多、千粒重偏低等特点。相关分析表明,西藏青稞各农艺性状间存在复杂的相关性,如穗粒数与株高、单株有效穗数与穗长、总小穗与穗长等呈显著或极显著的正相关和偏相关,单株有效穗数与株高呈极显著的负相关,千粒重与单株有效穗数呈极显著的负偏相关。主成分分析将参试的34份青稞材料的7个农艺性状分为4个主成分,其累积贡献率为91.192%,穗型的贡献率最高,达到46.4338%。供试材料在遗传距离5.18水平上可聚为三大类型：矮秆短穗少粒型、长穗多粒型、穗多粒重型。     

Comparison of infection with Fusarium head blight and accumulation of mycotoxins in grain of hulless and covered barley

We have evaluated 145 covered and 29 hulless barley genotypes artificially infected with Fusarium graminearum Schw. in a field experiment. Significant genetic variation for Fusarium head blight severity measured by the area under the disease progress curve and for mycotoxin contamination was found among covered and hulless barley lines. The overall mean area under the disease progress curve of covered and hulless barley did not differ significantly. Twenty-nine hulless-covered pairs with approximately the same disease severity were chosen for analysis of mycotoxins (B-trichothecenes) in the harvested grain. The average content of deoxynivalenol of the 29 covered and 29 hulless barley samples was 15,520 and 12,964 μg kg⁻¹, respectively. The mean deoxynivalenol, 3-acetyl-deoxynivalenol and 15-acetyl-deoxynivalenol content of covered barley was significantly higher than that of hulless barleys (p<0.01), whereas for nivalenol there was no significant difference between the mean values of covered and hulless barley. Hulless barley appears to be less prone to accumulation of mycotoxins in the harvested crop than covered barley most likely because a considerable proportion of the mycotoxin resides in the barley hulls.