A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat.

BACKGROUND: Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments. RESULTS: We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection. CONCLUSION: Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.

Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits.

BACKGROUND: Plant architecture associated with increased grain yield and adaptation to the local environments is selected during wheat (Triticum aestivum) breeding. The internode length of individual stems and tiller length of individual plants are important for the determination of plant architecture. However, few studies have explored the genetic basis of these traits. RESULTS: Here, we conduct a genome-wide association study (GWAS) to dissect the genetic basis of geographical differentiation of these traits in 306 worldwide wheat accessions including both landraces and traditional varieties. We determine the changes of haplotypes for the associated genomic regions in frequency in 831 wheat accessions that are either introduced from other countries or developed in China from last two decades. We identify 83 loci that are associated with one trait, while the remaining 247 loci are pleiotropic. We also find 163 associated loci are under strong selective sweep. GWAS results demonstrate independent regulation of internode length of individual stems and consistent regulation of tiller length of individual plants. This makes it possible to obtain ideal haplotype combinations of the length of four internodes. We also find that the geographical distribution of the haplotypes explains the observed differences in internode length among the worldwide wheat accessions. CONCLUSION: This study provides insights into the genetic basis of plant architecture. It will facilitate gene functional analysis and molecular design of plant architecture for breeding.

Population genomics unravels the Holocene history of bread wheat and its relatives.

Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.

Overexpression of FaHSP17.8-CII improves cadmium accumulation and tolerance in tall fescue shoots by promoting chloroplast stability and photosynthetic electron transfer of PSII.

Genetic improvement could play a significant role in enhancing the Cd accumulation, translocation and tolerance in plants. In this study, for the first time, we constructed transgenic tall fescue overexpressing a class II (CII) sHSP gene FaHSP17.8-CII, which enhanced Cd tolerance and the root-to-shoot Cd translocation. After exposed to 400 µM CdCl2, two FaHSP17.8-CII overexpressing lines (OE#3 and OE#7) exhibited 30% and 40% more shoot fresh weight, respectively, relative to the wild-type (WT). Both transgenic lines showed higher tolerance to Cd, as evidenced by lower levels of electrolyte leakage and malondialdehyde compared to the WT plants under Cd stress. FaHSP17.8-CII overexpression increased shoot Cd contents 49-59% over the WT plants. The Cd translocation factor of root-to-shoot in OE grasses was 69-85% greater than WT under Cd stress. Furthermore, overexpression of FaHSP17.8-CII reduced Cd-induced damages of chloroplast ultra-structure and chlorophyll synthesis, and then improved photosystem II (PSII) function under Cd stress, which resulted in less reactive oxygen species (ROS) accumulation in OE grasses than that in WT exposed to Cd stress. The study suggests a novel FaHSP17.8-CII-PSII-ROS module to understand the mechanisms of Cd detoxification and tolerance, which provides a new strategy to improve phytoremediation efficiency in Cd-stressed grasses.

Stress memory gene FaHSP17.8-CII controls thermotolerance via remodeling PSII and ROS signaling in tall fescue.

High temperature is the most limiting factor in the growth of cool-season turfgrass. To cope with high-temperature stress, grass often adopt a memory response by remembering one past recurring stress and preparing a quicker and more robust reaction to the next stress exposure. However, little is known about how stress memory genes regulate the thermomemory response in cool-season turfgrass. Here, we characterized a transcriptional memory gene, Fa-heat shock protein 17.8 Class II (FaHSP17.8-CII) in a cool-season turfgrass species, tall fescue (Festuca arundinacea Schreb.). The thermomemory of FaHSP17.8-CII continued for more than 4 d and was associated with a high H3K4me3 level in tall fescue under heat stress (HS). Furthermore, heat acclimation or priming (ACC)-induced reactive oxygen species (ROS) accumulation and photosystem II (PSII) electron transport were memorable, and this memory response was controlled by FaHSP17.8-CII. In the fahsp17.8-CII mutant generated using CRISPR/Cas9, ACC+HS did not substantially block the ROS accumulation, the degeneration of chloroplast ultra-structure, and the inhibition of PSII activity compared with HS alone. However, overexpression of FaHSP17.8-CII in tall fescue reduced ROS accumulation and chloroplast ultra-structure damage, and improved chlorophyll content and PSII activity under ACC+HS compared with that HS alone. These findings unveil a FaHSP17.8-CII-PSII-ROS module regulating transcriptional memory to enhance thermotolerance in cool-season turfgrass.

Simultaneous gene editing of three homoeoalleles in self-incompatible allohexaploid grasses.

Clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has been widely used for precise gene editing in plants. However, simultaneous gene editing of multiple homoeoalleles remains challenging, especially in self-incompatible polyploid plants. Here, we simultaneously introduced targeted mutations in all three homoeoalleles of two genes in the self-incompatible allohexaploid tall fescue, using both CRISPR/Cas9 and LbCas12a (LbCpf1) systems. Loss-of-function mutants of FaPDS exhibited albino leaves, while knockout of FaHSP17.9 resulted in impaired heat resistance in T0 generation of tall fescue. Moreover, these mutations were inheritable. Our findings demonstrate the feasibility of generating loss-of-function mutants in T0 generation polyploid perennial grasses using CRISPR/Cas systems.

Triticum population sequencing provides insights into wheat adaptation.

Bread wheat expanded its habitat from a core area of the Fertile Crescent to global environments within ~10,000 years. The genetic mechanisms of this remarkable evolutionary success are not well understood. By whole-genome sequencing of populations from 25 subspecies within the genera Triticum and Aegilops, we identified composite introgression from wild populations contributing to a substantial portion (4-32%) of the bread wheat genome, which increased the genetic diversity of bread wheat and allowed its divergent adaptation. Meanwhile, convergent adaptation to human selection showed 2- to 16-fold enrichment relative to random expectation-a certain set of genes were repeatedly selected in Triticum species despite their drastic differences in ploidy levels and growing zones, indicating the important role of evolutionary constraints in shaping the adaptive landscape of bread wheat. These results showed the genetic necessities of wheat as a global crop and provided new perspectives on transferring adaptive success across species for crop improvement.

The ethylene responsive factor CdERF1 from bermudagrass (Cynodon dactylon) positively regulates cold tolerance.

Cold stress is one of the major environmental factors that limit growth and utilization of bermudagrass [Cynodon dactylon (L.) Pers], a prominent warm-season turfgrass. However, the molecular mechanism of cold response in bermudagrass remains largely unknown. In this study, we characterized a cold-responsive ERF (ethylene responsive factor) transcription factor, CdERF1, from bermudagrass. CdERF1 expression was induced by cold, drought and salinity stresses. The CdERF1 protein was nucleus-localized and encompassed transcriptional activation activity. Transgenic Arabidopsis plants overexpressing CdERF1 showed enhanced cold tolerance, whereas CdERF1-underexpressing bermudagrass plants via virus induced gene silencing (VIGS) method exhibited reduced cold resistance compared with control, respectively. Under cold stress, electrolyte leakage (EL), malondialdehyde (MDA), H2O2 and O2- contents were reduced, while the activities of SOD and POD were elevated in transgenic Arabidopsis. By contrast, these above physiological indicators in CdERF1-underexpressing bermudagrass exhibited the opposite trend. To further explore the possible molecular mechanism of bermudagrass cold stress response, the RNA-Seq analyses were performed. The result indicated that overexpression of CdERF1 activated a subset of stress-related genes in transgenic Arabidopsis, such as CBF2, pEARLI1 (lipid transfer protein), PER71 (peroxidase) and LTP (lipid transfer protein). Interestingly, under-expression of CdERF1 suppressed the transcription of many genes in CdERF1-underexpressing bermudagrass, also including pEARLI1 (lipid transfer protein) and PER70 (peroxidase). All these results revealed that CdERF1 positively regulates plant cold response probably by activating stress-related genes, PODs, CBF2 and LTPs. This study also suggests that CdERF1 may be an ideal candidate in the effort to improve cold tolerance of bermudagrass in the further molecular breeding.

Antioxidant Metabolism, Photosystem II, and Fatty Acid Composition of Two Tall Fescue Genotypes With Different Heat Tolerance Under High Temperature Stress.

Tall fescue (Festuca arundinacea Schreb.) is a typical and widely used cool-season turf grass. High temperature is a key factor that limits its utility. The objectives of this study were to investigate the behaviors of fatty acid composition and its gene expression patterns in heat-resistant genotype "TF71" and heat-sensitive genotype "TF133" exposed to heat stress (40/35°C, 14/10 h), and to broaden our comprehension about the relationship between heat tolerance and fatty acid function. The result showed that heat stress increased the malondialdehyde (MDA) content and relative electrolyte leakage (EL), but decreased the level of chlorophyll and the activity of superoxide dismutase (SOD) and peroxidase (POD) when compared to the controls, to a greater extent in "TF133." This result proved that "TF71" had superior high-temperature resistance. Furthermore, comparing the changes in the composition of fatty acid and the expression of the genes involved in its synthesis between the two different genotypes under heat stress, we found that heat stress increased the degree of unsaturation, UFA/SFA, and double bond index (DBI) in "TF71." Moreover, quantitative RT-PCR revealed that heat stress altered the expression of the genes involved in fatty acid synthesis, including ACAC, FabD, FabF, FabH, FabI, and FatA. According to these findings, we can speculate that increasing the unsaturation degree of fatty acid or controlling the equilibrium ratio of UFA/SFA might be closely associated with the improving of the heat resistance in tall fescue.

Exogenous Calcium Enhances the Photosystem II Photochemistry Response in Salt Stressed Tall Fescue.

Calcium enhances turfgrass response to salt stress. However, little is known about PSII photochemical changes when exogenous calcium was applied in salinity-stressed turfgrass. Here, we probe into the rearrangements of PSII electron transport and endogenous ion accumulation in tall fescue (Festuca arundinacea Schreber) treated with exogenous calcium under salt stress. Three-month-old seedlings of genotype "TF133" were subjected to the control (CK), salinity (S), salinity + calcium nitrate (SC), and salinity + ethylene glycol tetraacetic acid (SE). Calcium nitrate and ethylene glycol tetraacetic acid was used as exogenous calcium donor and calcium chelating agent respectively. At the end of a 5-day duration treatment, samples in SC regime had better photochemistry performance on several parameters than salinity only. Such as the Area (equal to the plastoquinone pool size), N (number of [Formula: see text] redox turnovers until Fm is reached), ψE0, or δRo (Efficiencdy/probability with which a PSII trapped electron is transferred from QA to QB or PSI acceptors), ABS/RC (Absorbed photon flux per RC). All the above suggested that calcium enhanced the electron transfer of PSII (especially beyond [Formula: see text]) and prevented reaction centers from inactivation in salt-stressed tall fescue. Furthermore, both grass shoot and root tissues generally accumulated more C, N, Ca2+, and K+ in the SC regime than S regime. Interrelated analysis indicated that ψE0, δRo, ABS/RC, C, and N content in shoots was highly correlated to each other and significantly positively related to Ca2+ and K+ content in roots. Besides, high salt increased ATP6E and CAMK2 transcription level in shoot at 1 and 5 day, respectively while exogenous calcium relieved it. In root, CAMK2 level was reduced by Salinity at 5 day and exogenous calcium recovered it. These observations involved in electron transport capacity and ion accumulation assist in understanding better the protective role of exogenous calcium in tall fescue under salt stress.

Melatonin Is Involved in Regulation of Bermudagrass Growth and Development and Response to Low K+ Stress.

Melatonin (N-acetyl-5-methoxytryptamine) plays critical roles in plant growth and development and during the response to multiple abiotic stresses. However, the roles of melatonin in plant response to K+ deficiency remain largely unknown. In the present study, we observed that the endogenous melatonin contents in bermudagrass were remarkably increased by low K+ (LK) treatment, suggesting that melatonin was involved in bermudagrass response to LK stress. Further phenotype analysis revealed that exogenous melatonin application conferred Bermudagrass enhanced tolerance to LK stress. Interestingly, exogenous melatonin application also promoted bermudagrass growth and development at normal condition. Furthermore, the K+ contents measurement revealed that melatonin-treated plants accumulated more K+ in both shoot (under both control and LK condition) and root tissues (under LK condition) compared with those of melatonin non-treated plants. Expression analysis indicated that the transcripts of K+ transport genes were significantly induced by exogenous melatonin treatment in bermudagrass under both control and LK stress conditions, especially under a combined treatment of LK stress and melatonin, which may increase accumulation of K+ content profoundly under LK stress and thereby contributed to the LK-tolerant phenotype. In addition, we investigated the role of melatonin in the regulation of photosystem II (PSII) activities under LK stress. The chlorophyll fluorescence transient (OJIP) curves were obviously higher in plants grown in LK with melatonin (LK+Mel) than those of plants grown in LK medium without melatonin application for 1 or 2 weeks, suggesting that melatonin plays important roles in PSII against LK stress. After a combined treatment of LK stress and melatonin, the values for performance indexes (PIABS, PITotal, and PICS), flux ratios (φP0, ΨE0, and φE0) and specific energy fluxes (ETO/RC) were significantly improved compared with those of LK stress alone, suggesting that melatonin plays positive roles in protecting PSII activity under LK stress. Collectively, this study reveals an important role of melatonin in regulating bermudagrass response to LK stress.

Photosynthesis, antioxidant system and gene expression of bermudagrass in response to low temperature and salt stress.

There is widespread distribution of salinized lands in northern China. Harnessing such land is essential to environmental health. Bermudagrass [Cynodon dactylon (L.) Pers.] has the potential to improve the salinized lands. However, low temperature remarkably limits the growth of bermudagrass in winter. Currently, there is no information about the interaction of cold and salt in this plant. Hence, the objectives of this study were to figure out the effects of combined cold and salinity stress on bermudagrass. In this study, 4 °C and 200 mM salt solution was used as cold and salt treatments respectively while 4 °C along with 200 mM salt solution were applied as combined stress. After 5 days treatment, bermudagrass displayed a dramatic decline in the turf quality and chlorophyll content, but higher malonaldehyde, electrolyte leakage, hydrogen peroxide content, antioxidant enzyme activity in the combined stress regime as compared to cold or salt treated alone. Analysis of chlorophyll a revealed that the combined stress aggravated stress-induced inhibition of photosystem II. In addition, the expressions of stress-related genes were up-regulated with a lower expression level when cold and salt applied together. In summary, the grass exposed to combined stress presented a relatively lower stress tolerance and suffered a more severe damage than grass grown in the other regimes. These findings are crucial for elucidating the molecular mechanisms of cold and salt combined stress in bermudagrass, and provide information for breeding programs to select and develop bermudagrass cultivars that are suitable for improvement of the northern China salinized land.

Differential Acclimation of Enzymatic Antioxidant Metabolism and Photosystem II Photochemistry in Tall Fescue under Drought and Heat and the Combined Stresses.

Quality inferiority in cool-season turfgrass due to drought, heat, and a combination of both stresses is predicted to be more prevalent in the future. Understanding the various response to heat and drought stress will assist in the selection and breeding of tolerant grass varieties. The objective of this study was to investigate the behavior of antioxidant metabolism and photosystem II (PSII) photochemistry in two tall fescue genotypes (PI 234881 and PI 578718) with various thermotolerance capacities. Wide variations were found between heat-tolerant PI 578718 and heat-sensitive PI 234881 for leaf relative water content, malondialdehyde and electrolyte leakage under drought, high-temperature or a combination of both stresses. The sensitivity of PI 234881 exposed to combined stresses was associated with lower superoxide dismutase activity and higher H2O2 accumulation than that in PI 578718. Various antioxidant enzymes displayed positive correlation with chlorophyll content, but negative with membrane injury index at most of the stages in both tall fescue genotypes. The JIP-test analysis in PI 578718 indicated a significant improvement in ABS/RC, TR0/RC, RE0/RC, RE0/ABS values as compared to the control regime, which indicated that PI 578718 had a high potential to protect the PSII system under drought and high temperature stress. And the PS II photochemistry in PI 234881 was damaged significantly compared with PI578718. Moreover, quantitative RT-PCR revealed that heat and drought stresses deduced the gene expression of psbB and psbC, but induced the expression of psbA. These findings to some extent confirmed that the various adaptations of physiological traits may contribute to breeding in cold-season turfgrass in response to drought, high-temperature, and a combination of both stresses.