Deciphering genetic basis of developmental and agronomic traits by integrating high-throughput optical phenotyping and genome-wide association studies in wheat

Dissecting the genetic basis of complex traits such as dynamic growth and yield potential is a major challenge in crops. Monitoring the growth throughout growing season in a large wheat population to uncover the temporal genetic controls for plant growth and yield-related traits has so far not been explored. In this study, a diverse wheat panel composed of 288 lines was monitored by a non-invasive and high-throughput phenotyping platform to collect growth traits from seedling to grain filling stage and their relationship with yield-related traits was further explored. Whole genome re-sequencing of the panel provided 12.64 million markers for a high-resolution genome-wide association analysis using 190 image-based traits and 17 agronomic traits. A total of 8327 marker-trait associations were detected and clustered into 1605 quantitative trait loci (QTLs) including a number of known genes or QTLs. We identified 277 pleiotropic QTLs controlling multiple traits at different growth stages which revealed temporal dynamics of QTLs action on plant development and yield production in wheat. A candidate gene related to plant growth that was detected by image traits was further validated. Particularly, our study demonstrated that the yield-related traits are largely predictable using models developed based on i-traits and provide possibility for high-throughput early selection, thus to accelerate breeding process. Our study explored the genetic architecture of growth and yield-related traits by combining high-throughput phenotyping and genotyping, which further unravelled the complex and stage-specific contributions of genetic loci to optimize growth and yield in wheat.     

利用RIL群体进行小麦品质性状及其与产量性状的相关分析

利用小麦重组自交系(RIL)群体,对小麦主要品质性状、及其与产量的关系进行了分析。结果表明,RIL群体品质、产量性状都表现了较大的变异幅度;蛋白质各性状内、淀粉各性状内相关性多数显著,但二者之间相关性多不显著,这说明在小麦品种改良中,优良的蛋白质性状和优良的淀粉性状可以兼得;稳定时间、沉降值等重要的加工品质性状和淀粉性状与产量相关不显著,说明加工品质可以与产量很好地协调起来;适当降低千粒重,增加穗数,有利于强筋的形成和粘度的提高;矮杆、半矮杆性状能够与良好的加工品质、高蛋白质含量、高GMP含量协调起来。     

Rice siR109944 suppresses plant immunity to sheath blight and impacts multiple agronomic traits by affecting auxin homeostasis

Plant small RNAs (sRNAs) play significant roles in regulating various developmental processes and hormone signalling pathways involved in plant responses to a wide range of biotic and abiotic stresses. However, the functions of sRNAs in response to rice sheath blight remain unclear. We screened rice (Oryza sativa) sRNA expression patterns against Rhizoctonia solani and found that Tourist‐miniature inverted‐repeat transposable element (MITE)‐derived small interfering RNA (siRNA) (here referred to as siR109944) expression was clearly suppressed upon R. solani infection. One potential target of siR109944 is the F‐Box domain and LRR‐containing protein 55 (FBL55), which encode the transport inhibitor response 1 (TIR1)‐like protein. We found that rice had significantly enhanced susceptibility when siR109944 was overexpressed, while FBL55 OE plants showed resistance to R. solani challenge. Additionally, multiple agronomic traits of rice, including root length and flag leaf inclination, were affected by siR109944 expression. Auxin metabolism‐related and signalling pathway‐related genes were differentially expressed in the siR109944 OE and FBL55 OE plants. Importantly, pre‐treatment with auxin enhanced sheath blight resistance by affecting endogenous auxin homeostasis in rice. Furthermore, transgenic Arabidopsis overexpressing siR109944 exhibited early flowering, increased tiller numbers, and increased susceptibility to R. solani. Our results demonstrate that siR109944 has a conserved function in interfering with plant immunity, growth, and development by affecting auxin homeostasis in planta. Thus, siR109944 provides a genetic target for plant breeding in the future. Furthermore, exogenous application of indole‐3‐acetic acid (IAA) or auxin analogues might effectively protect field crops against diseases.     

Genome‐wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China

Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here, we revealed new allelic variation distribution for 13 yield‐related traits in series of genome‐wide association studies (GWAS) using the wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over 3 years. After filtering SNP data sets, GWAS using 20 689 high‐quality SNPs associated 1769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions. Of these, repetitive and pleiotropic SNPs on chromosomes 6AS, 6AL, 6BS, 5BL and 7AS were significantly linked to thousand kernel weight, for example BS00021705_51 on 6BS and wsnp_Ex_c32624_41252144 on 6AS, with phenotypic variation explained (PVE) of ~24%, consistently identified in 12 and 13 of the 14 environments, respectively. Kernel length‐related SNPs were mainly identified on chromosomes 7BS, 6AS, 5AL and 5BL. Plant height‐related SNPs on chromosomes 4DS, 6DL, 2DS and 1BL were, respectively, identified in more than 11 environments, with averaged PVE of ~55%. Four SNPs were confirmed to be important genetic loci in two RIL populations. Based on repetivity and PVE, a total of 41 SNP loci possibly played the key role in modulating yield‐related traits of the cultivars surveyed. Distribution of superior alleles at the 41 SNP loci indicated that superior alleles were getting popular with time and modern cultivars had integrated many superior alleles, especially for peduncle length‐ and plant height‐related superior alleles. However, there were still 19 SNP loci showing less than percentages of 50% in modern cultivars, suggesting they should be paid more attention to improve yield‐related traits of cultivars in the Yellow and Huai wheat region. This study could provide useful information for dissection of yield‐related traits and valuable genetic loci for marker‐assisted selection in Chinese wheat breeding programme.     

Genome‐wide association study of six quality traits reveals the association of the TaRPP13L1 gene with flour colour in Chinese bread wheat

Flour colour, kernel hardness, grain protein content and wet gluten content are important quality properties that determine end use in bread wheat. Here, a wheat 90K genotyping assay was used for a genome‐wide association study (GWAS) of the six quality‐related traits in Chinese wheat cultivars in eight environments over four years. A total of 846 significant single nucleotide polymorphisms (SNPs) were identified, explaining approximately 30% of the phenotypic variation on average, and 103 multienvironment‐significant SNPs were detected in more than four environments. Quantitative trait loci (QTL) mapping in the biparent population confirmed some important SNP loci. Moreover, it was determined that some important genes were associated with the six quality traits, including some known functional genes and annotated unknown functional genes. Of the annotated unknown functional genes, it was verified that TaRPP13L1 was associated with flour colour. Wheat cultivars or lines with TaRPP13L1‐B1a showed extremely significantly higher flour redness and lower yellowness than those with TaRPP13L1‐B1b in the Chinese wheat natural population and the doubled haploid (DH) population. Two tetraploid wheat lines with premature stop codons of the TaRPP13L1 gene mutagenized by ethyl methanesulfonate (EMS) showed extremely significantly higher flour redness and lower yellowness than wild type. Our data suggest that the TaRPP13L1 gene plays an important role in modulating wheat flour colour. This study provides useful information for further dissection of the genetic basis of flour colour and also provides valuable genes or genetic loci for marker‐assisted selection to improve the process of breeding quality wheat in China.     

The plant growth-promoting rhizobacterium Bacillus cereus AR156 induces resistance in tomato with induction and priming of defence response

In a previous study, we demonstrated the ability of the rhizobacterium Bacillus cereus AR156 (AR156) to protect tomato against bacterial wilt caused by Ralstonia solanacearum and root-knot disease caused by Meloidogyne incognita. Here, we investigate the ability of AR156 to promote plant growth and its role in the systemic protection of tomatoes cultivated in greenhouses against bacterial speck disease caused by Pseudomonas syringae pv. tomato DC3000 (DC3000). In our experiments, the AR156 population reached 10⁵–10⁶ CFU/g rhizosphere soil, and remained at that level in the rhizosphere of tomato plants for more than 2 months. In terms of its ability to promote plant growth, AR156 increased the average biomass of the tomato by 47.7%. AR156 also elicited induced systemic resistance against DC3000, significantly reduced bacterial speck disease severity 1.6-fold, and inhibited proliferation of the pathogen by approximately 15-fold. This strain triggered the accumulation of defence-related genes (PR1 and PIN2) in tomato leaves and primed the leaves for accelerated defence-related gene expression upon challenge with DC3000. That suggested simultaneous activation of the salicylic acid and the jasmonic acid dependent signalling pathways by AR156 against DC3000. In conclusion, B. cereus AR156 was found to form robust colonies in the roots of tomato and had some beneficial effects, including biological control of bacterial speck disease via ISR and promotion of plant growth.     

Identification of multiple isoforms of soluble and granule-bound starch synthase in developing wheat endosperm

We have investigated the nature and locations of isoforms of starch synthase in the developing endosperm of wheat (Triticum aestivum L.). There are three distinct granule-bound isoforms of 60 kDa (the Waxy gene product), 77 kDa and 100–105 kDa. One of these isoforms, the 77-kDa protein, is also present in the soluble fraction of the endosperm but it contributes only a small proportion of the total soluble activity. Most of the soluble activity is contributed by isoforms which are apparently not also granule-bound. The 60-kDa and 77kDa isoforms of wheat are antigenically related to isoforms of very similar size in the developing pea embryo, but the other isoforms in the endosperm appear to have no counterparts in the pea embryo. The significance of these results in terms of the diversity of isoforms of starch synthase and their locations is discussed.Abbreviations DEAE diethylaminoethyl - GBSS granule-bound starch synthase - NT nullisomictetrasomic We are grateful to the late John Hawker (University of Adelaide, Australia) and to John Snape (John Innes Centre, UK) for useful discussions during the course of this work, to John Snape and Catherine Chinoy (John Innes Centre, UK) for the gift of the NT lines and to Richard Batt (University of Adelaide, Australia) for technical assistance.     

PFCA uptake and translocation in dominant wheat species (Triticum aestivum L.)

The comparative uptake of four perfluorinated carboxylic acids (PFCAs) by wheat (Triticum aestivum L.) grown in nutrient solution was investigated. Wheat is the main food crop in northern China and may become a potential pathway of human exposure to these PFCAs. The uptake of four PFCAs from water at a fixed concentration (1 μg/mL) increased over time, approaching a steady state, and except for the short-chain perfluorobutanoic acid, most of the total mass of each of the PFCAs taken up by wheat was found to be at the root. The root concentration factor (RCF) and shoot/root concentration factor (SRCF) were calculated, and with the increase in carbon chain length, the RCFs increased but SRCFs decreased, which indicated that long-chain PFCAs had stronger root uptake and weaker translocation capacities than short-chain PFCAs. In addition, pH could obviously impact the uptake of four PFCAs in the roots and shoots of wheat, and the highest concentrations were found at pH = 7 when the pH increased from 4 to 10.     

Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations

Though epistasis has long been postulated to have a critical role in genetic regulation of important pathways as well as provide a major source of variation in the process of speciation, the importance of epistasis for genomic selection in the context of plant breeding is still being debated. In this paper, we report the results on the prediction of genetic values with epistatic effects for 280 accessions in the Nebraska Wheat Breeding Program using adaptive mixed least absolute shrinkage and selection operator (LASSO). The development of adaptive mixed LASSO, originally designed for association mapping, for the context of genomic selection is reported. The results show that adaptive mixed LASSO can be successfully applied to the prediction of genetic values while incorporating both marker main effects and epistatic effects. Especially, the prediction accuracy is substantially improved by the inclusion of two-locus epistatic effects (more than onefold in some cases as measured by cross-validation correlation coefficient), which is observed for multiple traits and planting locations. This points to significant potential in using non-additive genetic effects for genomic selection in crop breeding practices.     

Simulating the effects of localized red:far-red ratio on tillering in spring wheat (Triticum aestivum) using a three-dimensional virtual plant model

The outgrowth of tiller buds in Poaceae is influenced by the ratio of red to far-red light irradiance (R:FR). At each point in the plant canopy, R:FR is affected by light scattered by surrounding plant tissues. This paper presents a three-dimensional virtual plant modelling approach to simulate local effects of R:FR on tillering in spring wheat (Triticum aestivum). R:FR dependence of bud outgrowth was implemented in a wheat model, using three hypothetical responses of bud extension to R:FR (unit step, curvilinear and linear response). Bud break occurred when a threshold bud length was reached. Simulations were performed for three plant population densities. In accordance with experimental observations, fewer tillers per plant were simulated for higher plant population densities. The linear and curvilinear responses caused a delay in the increase in tiller number compared with experimental data. The unit step response approached experimental results best. It is suggested that a model based on relatively simple relations can be used to simulate degree of tillering. This study has shown that the virtual plant approach is a promising tool with which to address crop morphological and ecological research questions where the determining factors act at the level of the individual plant organ.     

基于DSSAT模型的长江中下游冬小麦潜在产量模拟研究

为了探明气候变化对长江中下游地区冬小麦潜在产量的影响,基于政府间气候变化专门委员会(IPCC)AR5提出的BCCCSM1-1(Beijing Climate Center Climate System Model version1-1)气候系统模式输出的基于典型浓度RCP各情景(基准时段baseline、RCP 2.6、RCP 4.5和RCP 8.5)主要气象要素的逐日模拟数据和历史观测数据。通过DSSAT模型模拟历史时期(2001—2009年)冬小麦的物候期和产量,并计算模拟数据与实测数据二者的均方根误差和一致性指数(开花、成熟期和产量模拟结果的相对均方差根误差分别在0.83%—2.98%之间和7%以下,符合度D均接近于1)明确最优遗传参数,应用最优参数模拟加以验证,完成模型参数区域化。结合历史阶段(1961—1990年)和未来时期(2021—2050年)主要气象要素变化趋势,利用DSSAT模型模拟分析未来30年长江中下游地区气候变化对小麦产量的影响及变化趋势,以期为未来作物生产提供理论依据。结果表明,DSSAT-CERES-Wheat品种遗传参数本地化后能准确模拟冬小麦的生长发育过程及产量潜力。较基准年相比,2021—2050年RCP情景下,冬小麦生育期内≥10℃积温除RCP 2.6情景外呈现逐渐增加趋势,增加幅度为RCP 8.5RCP 2.6RCP 4.5;降水量年际波动都比较大,区域性差异明显;太阳总辐射量较基准年均有所降低,但降低的幅度随着年份的增加逐渐减小,变化率均呈现显著或极显著的增加趋势。除昆山外冬小麦开花期、成熟期较基准年均有所提前,开花期到成熟期天数则随之缩短。仅考虑气候条件时,长江中下游地区冬小麦产量潜力与基准年减少,昆山、英山下降幅度较滁州、钟祥大(3%—59%),且区域差异明显。分析可得,一定范围内冬小麦产量随积温的增加逐渐增加,超过一定阈值时则逐渐减少,其他气候因子增加或减少并不能弥补积温过低产生的负效应。     

Divergent patterns of foliar δ13C and δ15N in Quercus aquifolioides with an altitudinal transect on the Tibetan Plateau: an integrated study based on multiple key leaf functional traits

Aims With a close association with plant water availability, foliar δ 13 C had been investigated extensively in alpine regions; however, foliar δ 15 N has rarely been concurrently used as an indicator of plant nitrogen availability. Due to the positive correlations between leaf nitrogen content and foliar δ 13 C and δ 15 N found in previous studies, we expected that they should show consistent patterns along an altitudinal gradient.Methods To test our hypothesis, we measured foliar δ 13 C and δ 15 N in conjunction with multiple key leaf functional traits of Quercus aquifolioides, a dominant species of alpine forest on the eastern slopes of the Sygera Mountains, southeastern Tibetan Plateau from 2500 to 3800 m.Important findings (i) Contrary to our hypothesis, foliar δ 13 C exhibited a significant positive linear relationship with altitude; in contrast, foliar δ 15 N initially increased and subsequently decreased with altitude, the change in trend occurring around 3300 m. (ii) Our analyses indicated that leaf internal resistance and stomatal conductance, rather than photosynthetic capacity indicated by leaf N concentration, apparently explained the altitudinal variation in foliar δ 13 C, while differences in foliar δ 15 N were likely the result of soil N availability. (iii) Principal component analysis revealed a clear association between δ 13 C and a tradeoff between water loss and carbon gain, indicated by traits related to gas exchange such as leaf thickness, density, stomatal properties. In contrast, the second axis was associated with δ 15 N and nitrogen acquisition strategy in Q. aquifolioides across its altitudinal distribution, represented by traits related to nitrogen concentration and stomata per gram of leaf nitrogen.