Rye (Secale cereale L.) has been widely used to improve wheat (Triticum aestivum L.) cultivars. Oligo probes combined with non-denaturing fluorescence in situ hybridization (ND-FISH) technology provide a convenient and efficient way to identify individual rye chromosomes. However, suitable ND-FISH-positive oligo probes for recognizing specific segments of rye chromosomes are lacking. Five new ND-FISH-positive oligo probes: Oligo-5BL.46, Oligo-5A8080, Oligo-5A8080.1, Oligo-1AL.73, and Oligo-0R3, combined with two previously reported oligo probes, Oligo-44 and Oligo-45, were used in this study. Probes Oligo-5BL.46, Oligo-5A8080 and Oligo-44 produced signals only in intercalary regions of arms 1RS, 5RS, and 5RL, respectively. Probe Oligo-5A8080.1 combined with probe Oligo-45 distinguished the intercalary regions of arms 1RS, 5RS, and 6RS simultaneously. Oligo-5A8080 and Oligo-5A8080.1 revealed variation in the distribution of 5S rDNA sequences and polymorphism among 5R chromosomes. Probe Oligo-1AL.73 produced signals only on chromosomes 4R and 7R and contributed to the construction of an improved FISH map of chromosome 4RKu and to the confirmation of 4RLKu breakpoints in wheat-rye 4RLKu translocation chromosomes. Oligo-0R3 produced signals in the telomeric and subtelomeric regions of 14 rye chromosomes. These oligo probes also revealed five new tandem repeats in rye. Using the oligo probes reported in this study, the short arms of 1R, 5R, and 6R and the long arms of 4R and 7R can be easily discriminated when these chromosomes are broken.
Seed moisture at harvest is a critical trait affecting maize quality and mechanized production, and is directly determined by the dehydration process after physiological maturity. However, the dynamic nature of seed dehydration leads to inaccurate evaluation of the dehydration process by conventional determination methods. Seed dry weight and fresh weight were recorded at 14 time points after pollination in a recombinant inbred line (RIL) population derived from two inbred lines with contrasting seed dehydration dynamics. The dehydration curves of RILs were determined by fitting trajectories of dry weight accumulation and dry weight/fresh weight ratio change based on a logistic model, allowing the estimation of eight characteristic parameters that can be used to describe dehydration features. Quantitative trait locus (QTL) mapping, taking these parameters as traits, was performed using multiple methods. Single-trait QTL mapping revealed 76 QTL associated with dehydration characteristic parameters, of which the phenotypic variation explained (PVE) was 1.03% to 15.24%. Multiple-environment QTL analysis revealed 21 related QTL with PVE ranging from 4.23% to 11.83%. Multiple-trait QTL analysis revealed 58 QTL, including 51 pleiotropic QTL. Combining these mapping results revealed 12 co-located QTL and the dehydration process of RILs was divided into three patterns with clear differences in dehydration features. These results not only deepen general understanding of the genetic characteristics of seed dehydration but also suggest that this approach can efficiently identify associated genetic loci in maize.
Extreme heat stress events are becoming more frequent under anticipated climate change, which can have devastating impacts on rice growth and yield. To quantify the effects of short-term heat stress at booting stage on nonstructural carbohydrates (NSC) remobilization in rice, two varieties (Nanjing 41 and Wuyunjing 24) were subjected to 32/22/27 °C (maximum/minimum/mean), 36/26/31 °C, 40/30/35 °C, and 44/34/39 °C for 2, 4 and 6 days in phytotrons at booting stage during 2014 and 2015. Yield and yield components, dry matter partitioning index (DMPI), NSC accumulation and translocation were measured and calculated. The results showed that the increase of high-temperature level and duration significantly reduced grain yield by suppressing spikelet number per panicle, seed-setting rate, and grain weight. Heat stress at booting decreased DMPI in panicles, increased DMPI in stems, but had no significant effect on photosynthetic rate. Stem NSC concentration increased whereas panicles NSC concentration, stem NSC translocation efficiency, and contribution of stem NSC to grain yield decreased. Severe heat stress even transformed the stem into a carbohydrate sink during grain filling. The heat-tolerant Wuyunjing 24 showed a higher NSC transport capacity under heat stress than the heat-sensitive Nanjing 41. Heat degree-days (HDD), which combines the effects of the intensity and duration of heat stress, used for quantifying the impacts of heat stress indicates the threshold HDD for the termination of NSC translocation is 9.82 °C day. Grain yield was negatively correlated with stem NSC concentration and accumulation at maturity, and yield reduction was tightly related to NSC translocation reduction. The results suggest that heat stress at booting inhibits NSC translocation due to sink size reduction. Therefore, genotypes with higher NSC transport capacity under heat stress could be beneficial for rice yield formation.
Root system architecture (RSA) contributes to nitrogen (N) uptake and utilization in maize. In this study, a germplasm enhancement of maize double haploid population of 226 lines genotyped with 61,634 SNPs was used to investigate the genetic basis of RSA under two N levels using a genome-wide association study (GWAS). GLM + PCA, FarmCPU, and MLM models were utilized to balance false positives and false negatives. In total, 33 and 51 significant SNP-trait associations were detected under high and low N conditions, respectively. Under high N, SNP S9_2483543 was detected by all models. Linkage disequilibrium (LD) regions of some SNPs overlapped with the intervals of QTL for RSA and N response that were detected in previous studies. In particular, several known genes, Rtcs, Rtcl, Rtcl, and Ms44, were located in the LD regions of S1_9992325, S9_151726472, S9_154381179, and S4_197073985, respectively. Among the candidate genes identified by this study, GRMZM2G139811, GRMZM2G314898, GRMZM2G054050, GRMZM2G173682, GRMZM2G470914, GRMZM2G462325, GRMZM2G416184, and GRMZM2G064302 were involved in seedling, seed, and root system development or N metabolism in Arabidopsis or rice. The markers identified in this study can be used for marker-assisted selection of RSA traits to improve nitrogen use efficiency in maize breeding, and the candidate genes will contribute to further understanding of the genetic basis of RSA under diverse N conditions.
On the basis of growing environment, maize can largely be classified into temperate and tropical groups, leaving extensive genetic variation and evolutionary signatures in the maize genome. To identify candidate genes governing flowering time and photoperiod sensitivity, selective signature analysis and SNP- and haplotype-based GWAS were performed using 39,350 high-quality SNP markers in temperate and tropical maize groups consisting of 410 inbred lines phenotyped in three representative experiments in different latitudes. Selective signature analysis revealed 106 selective-sweep regions containing 423 candidate genes involved mainly in biological regulation and biosynthesis pathways. Among these genes, 25 overlapped with known genes governing flowering time and photoperiod sensitivity and 37 were also detected by GWAS for days to tassel, anthesis-silk interval, and photoperiod sensitivity measured by days to silking. Only two of the candidate genes governing flowering time overlapped selective signals. Most haplotype alleles within significant haplotype loci showed the same direction of effect on flowering time and photoperiod sensitivity. The inbred lines carrying GATT at HapL499 (haplotype locus 499) on chromosome 1 had relatively short flowering times. Lines carrying CA at HapL4054 on chromosome 10, TA at HapL4055 on chromosome 10, and GTTGT at HapL978 on chromosome 2 were less sensitive to photoperiod than lines carrying other haplotype alleles. Haplotype loci associated with flowering time and photoperiod sensitivity explained respectively 17.5%-18.6% and 11.2%-15.5% of phenotypic variation. Candidate genes and favorable haplotypes identified in this study may support the more efficient utilization of maize germplasm groups.
Plant height has been a major target for selection of high-yielding varieties in wheat. Two height-reducing loci (Rht-B1 and Rht-D1) have been widely used since the Green Revolution. However, these genes also negatively affect other agronomic traits such as kernel weight. Identifying alternative height-reducing loci could benefit wheat improvement. This study focused on the genetics of plant height in 260 historical and contemporary winter wheat accessions via genome-wide association studies using 38,693 single nucleotide polymorphism (SNP) markers generated through genotyping by sequencing, two Kompetitive Allele Specific Polymorphism markers, and phenotypic data recorded in two seasons (2016 and 2018). The 260 accessions showed wide variation in plant height. Most accessions developed after 1960 were shorter than earlier accessions. The broad-sense heritability for plant height was high (H2 = 0.82), which was also supported by a high correlation (r = 0.82, P < 0.0001) between heights from the two years. We detected a total of 16 marker-trait associations (MTAs) for plant height at -lg (P) ≥ 4.0 on chromosomes 1A, 2B, 2D, 3B, 4D, 5A, 5D, 6A, 6B, 7A, and 7D. We detected three of the MTAs (QPLH-2D, QPLH-4B.2, and QPLH-4D) consistently in individual-year and combined-year analyses. These MTAs individually explained 10%-16% of phenotypic variation. The height-reducing alleles at these three MTAs appeared after 1960 and increased in frequency thereafter. Among the genes near these loci were gibberellic acid insensitive (GAI) and GRAS transcription factor (GIBBERELLIC-ACID INSENSITIVE (GAI), REPRESSOR of GAI (RGA), and SCARECROW (SCR)). The evidence from this study and previous reports suggests that QPLH-2D is Rht8. A gene encoding a GRAS transcription factor is located near QPLH-2D. Validation of the QPLH-2D locus and associated candidate genes awaits further study.
Triticum urartu, a diploid wild wheat and progenitor of the A genome of bread wheat, is an important resource for resistance to powdery mildew fungus caused by Blumeria graminis f. sp. tritici (Bgt). In the present study we systematically characterized the interaction between the Bgt fungus and T. urartu at the microscopic level. We also tested 227 T. urartu accessions for reaction to Bgt isolate E09 and discovered previously uncategorized powdery mildew resistance in this collection. Pm60 is a CC-NB-LRR type powdery mildew resistance gene that has at least three functional alleles, Pm60, Pm60a, and Pm60b. A marker-assisted screen targeting the Pm60 locus identified a non-functional allele of Pm60a, designated as Pm60a′. A sequence comparison of Pm60a′ and Pm60a revealed that they differed by 58 SNPs and one 3-nucleotide deletion. Based on the sequence variations two molecular markers were developed to differentiate the functional Pm60a allele from the non-functional Pm60a′. Our screen revealed the presence of a previously uncharacterized powdery mildew resistance in T. urartu and provides new insights into the Pm60 locus. We believe that the two molecular markers developed here and new T. urartu resistant accessions will facilitate further identification of novel powdery mildew resistance genes and benefit breeding for powdery mildew resistance.
A fast-growing protein and oil crop, soybean was domesticated in ancient China and disseminated early in Asia and afterwards to other continents, in particular the Americas in recent centuries. After adaptation, locally developed landraces and cultivars formed a diversity of geographic-populations. In an investigation of their phylogeographic features, marker-derived traits were combined with geography-related photo- and temperature-sensitive traits to study 13 geographic-populations comprising 371 accessions. Extreme differentiation among geographic-populations was observed for flowering date (33-94 days), maturity date (79-181 days), and main stem node number (6-25 nodes). Restriction-site associated DNA sequencing revealed strong genetic differentiation among these geographic-populations, including genetic richness (alleles, 35,242-44,986) and specific-present alleles (SPAs, 0-67). More SPAs (28-67) emerged in some secondary and tertiary centers than in centers of origin (8-11). Phenotypic and genotypic clustering divided 11 of the 13 geographic-populations into the same five sets of sensitivity-similar geographic-populations and grouped the populations of northeast China and northern North America rather than center-of-origin populations as secondary centers, indicating the importance of geography-related traits in determining genetic differences among geographic-populations. A model of four soybean dissemination paths is presented: from the center of origin to the north, east, and south in Asia and from northeast China to Europe and the Americas. These findings provide a detailed phylogeographic understanding of worldwide soybeans.
Cotton fibers are the main raw materials of the textile industry. Exogenous superior fiber genes have been introduced into upland cotton to develop high-yield cultivars with excellent fiber quality. We used a single chromosomal segment on the chromosome A07 substitution line SL7, with high fiber strength, to investigate the molecular mechanism underlying its fiber quality. RNA-seq and KEGG analysis showed that 70 differentially expressed genes were enriched in plant hormone transduction pathways, including auxin, ethylene and abscisic acid, in fibers at 10 days post-anthesis (DPA). Among these, fiber-development related transcription factors MYB and NAC, including Gh_A11G0981 (MYB108), Gh_A03G0887 (NAC029), and Gh_A08G1691 (NAC021), were significantly upregulated in SL7, as were numerous cellulose synthase-like (CSL) genes involved in non-cellulose polysaccharide and cell wall synthesis. The hemicellulose content of SL7 was significantly higher than that of L22, an upland cotton cultivar. These results suggest that key genes in the introgressed chromosomal segment of SL7 regulate the expression of transcription-factor genes via hormone-transduction pathways, thereby inducing the expression of genes involved in secondary wall synthesis and ultimately improving fiber quality. This study has shed light on the molecular mechanism of fiber development and will contribute to the improvement of fiber quality of upland cotton by molecular breeding.
In vivo haploid induction based on maternal haploid inducers is the first step in deriving completely homozygous maize doubled haploid (DH) lines. Haploid induction rate (HIR) is influenced by both pollen parent inducing haploidy and the maternal source germplasm used in induction crosses. This study was aimed at analyzing the influence of source germplasm on HIR using 671 tropical inbred lines organized in two association mapping panels. These two association mapping panels (AMP1 and AMP2) were crossed to two different Tropically Adapted Inducer Lines (TAILs). For HIR assessment, seeds from induction crosses were planted in the field and ploidy status of each surviving plant was assessed using a gold standard classification based on visual differences between the haploid and diploid plants. The analysis revealed significant variation for HIR and led to identification of several tropical inbred lines that respond very positively to haploid induction. Use of HIR data in a genome wide association study (GWAS) led to identification of twenty-seven and two SNPs that were significantly associated with HIR in AMP1 and AMP2, respectively. Meta-analysis of AMP1 and AMP2 GWAS led to identification of 52 SNPs with significant effect on HIR across both studies. Genome-wide prediction revealed moderate to high prediction accuracy within AMPs using random SNPs. Inclusion of the SNPs detected in GWAS into the prediction model led to improvement in prediction accuracy. Overall, the study revealed that the maternal influence on HIR is controlled by a few moderate and many small effect QTL.
In higher plants, vacuolar invertases play essential roles in sugar metabolism, organ development, and sink strength. In sorghum (Sorghum bicolor), two vacuolar invertase genes, SbVIN1 (Sobic. 004G004800) and SbVIN2 (Sobic. 006G160700) have been reported, but their enzymatic properties and functional differences are largely unknown. We combined molecular, biochemical and genomic approaches to investigate their roles in sorghum stem and grain traits. SbVIN1 and SbVIN2 showed different expression levels in internodes, leaves, and panicles, indicating that their importance in each organ was different. In an in vitro sucrose hydrolysis assay, proteins of both genes heterologously expressed in Pichia pastoris displayed similar enzyme properties including the same optimum reaction pH (5) and similar Km for sucroe (49 mmol L−1 and 45 mmol L−1 for SbVIN1 and SbVIN2, respectively). The optimum reaction temperatures of SbVIN1 and SbVIN2 were 45 °C and 65 °C, respectively. SbVIN2 showed higher tolerance to high temperature than SbVIN1. We characterized the sequence variation of these two vacuolar invertase genes in a panel of 216 diverse inbred lines of sweet and grain sorghum and performed gene-based association analysis. SbVIN1 showed significant associations with stem traits including stem length, stem diameter, internode number, stem fresh weight, and Brix, as well as grain traits including hundred-grain weight and grain width. Significantly associated variation sites were mainly in 5′ upstream and intron regions. SbVIN2 only associated with grain width and stem water-soluble carbohydrates (WSCs) content. We conclude that the vacuolar invertase genes SbVIN1 and SbVIN2 are differently associated with stem and grain traits in sorghum.
Wheat is one of the most important staple crops worldwide. Fusarium head blight severely reduces wheat yield and quality. Cultivation of a novel type of cleistogamous wheat mutant, ZK001, which was created by static magnetic field treatment, is a new strategy for controlling Fusarium head blight. However, little is known about the mechanism of cleistogamy in wheat. The present study demonstrated that anthers of ZK001 were retained on the glumes at all flowering stages, whereas those of YM18 were extruded from the paleae and lemmae. There was a clear difference in the morphological characteristics of lodicules between YM18 and ZK001. Lodicule calcium and potassium contents were significantly higher in YM18 than in ZK001 from white to yellow anther stages. In Fusarium head blight resistance, the diseased kernel rate and deoxynivalenol content of ZK001 were markedly lower than those of YM18 and QM725. Comparative transcriptome analysis of YM18 and ZK001 was performed to identify regulatory mechanisms of cleistogamy. The main differentially expressed genes identified in the spikelets of YM18 and ZK001 at the green anther stage were associated with cell walls, carbohydrates, phytohormones, water channel, and ion binding, transport, and homeostasis. These differentially expressed genes may play an important role in regulating cellular homeostasis, osmotic pressure, and lodicule development. The results indicate that ZK001 lost the ability to push the lemmae and paleae apart during the flowering stage because of the thin lodicules. ZK001 was speculated to provide structural barriers for Fusarium head blight during the flowering stage. The thin lodicule of ZK001 results from low levels of soluble sugar, calcium ions, and potassium ions in the lodicules. These levels are regulated by differentially expressed genes.
Sustainable agriculture in the Huang-Huai-Hai Plain of China is threatened by subsoil compaction and the decline of winter wheat productivity induced by inappropriate tillage regimes. We investigated the effects of optimizing the tillage regime on grain filling and its relationship with flag leaf senescence post-anthesis in winter wheat. Four treatments were compared: rotary tillage, strip rotary tillage, strip rotary tillage with a 2-year subsoiling interval (STS), and conventional plowing tillage. STS produced higher chlorophyll content and leaf area indexes than other treatments, resulting in a greater photosynthetically active radiation capture ratio. The net photosynthesis rate of flag leaves from 14 to 28 days after anthesis and dry matter accumulation at maturity were higher in STS than in other treatments. Sucrose content and sucrose phosphate synthase activity of flag leaves first increased and then decreased during grain filling and were highest in STS. STS increased superoxide dismutase activity, increased soluble protein content, and reduced malondialdehyde concentrations in flag leaves after the middle grain-filling stages, resulting in reduced premature senescence. This consequence extended the active grain filling period and increased grain weight. The highest yields were observed in STS, reaching 10,451 kg ha−1 in 2014-2015 and 10,074 kg ha−1 in 2015-2016, owing to increased spike numbers and 1000-kernel weight. Overall, our study suggested that STS could substantially increase photosynthetic capacity and delay leaf senescence, thus promoting grain filling rate and increasing winter wheat yields.
Vitamin E, consisting of tocopherols and tocotrienols, serves as a lipid-soluble antioxidant in sweet corn kernels, providing nutrients to both plants and humans. Though the key genes involved in the vitamin E biosynthesis pathway have been identified in plants, the genetic architecture of vitamin E content in sweet corn kernels remains largely unclear. In the present study, an association panel of 204 inbred lines of sweet corn was constructed. Seven compounds of vitamin E were quantified in sweet corn kernels at 28 days after pollination. A total of 119 loci for vitamin E were identified using a genome-wide association study based on genotyping by sequencing, and a genetic network of vitamin E was constructed. Candidate genes identified were involved mainly in RNA regulation and protein metabolism. The known gene ZmVTE4, encoding γ-tocopherol methyltransferase, was significantly associated with four traits (α-tocopherol, α-tocotrienol, the α/γ-tocopherol ratio, and the α/γ-tocotrienol ratio). The effects of two causative markers on ZmVTE4 were validated by haplotype analysis. Finally, two elite cultivars (Yuetian 9 and Yuetian 22) with a 4.5-fold increase in the sum of α- and γ-tocopherols were developed by marker-assisted selection, demonstrating the successful biofortification of sweet corn. Three genes (DAHPS, ADT2, and cmu2) involved in chorismate and tyrosine synthesis were significantly associated with the α/γ-tocotrienol ratio. These results shed light on the genetic architecture of vitamin E and may accelerate the nutritional improvement of sweet corn.
Seed number (SN) is the component most strongly associated with yield in soybean. SN depends on pod number (PN) and seeds per pod (SPP). Whereas SPP is a relatively stable component, PN is strongly influenced by environmental and management factors. However, the environmental cues involved in PN regulation are not completely understood. The influence of increasing SPP on other yield components is controversial. Field trials were conducted in two growing seasons using two pairs of lanceolate (L) and ovate (O) near-isogenic lines, sown at low (LD) and high (HD) plant densities to evaluate the effect of leaflet shape on crop growth parameters, canopy red/far-red (R/FR) ratio, their relationships with pod initiation, PN, and yield; and the effect of increasing SPP on PN, SN, and yield. L canopies showed a higher number of pods initiated (PI) than O canopies owing to the increase of PI on branches. No association between PI and crop growth rate during the pod set period was found. PI was negatively associated with leaf area index (LAI) and light interception. In contrast, a positive association between PI and canopy R/FR ratio was found. This latter association was sustained irrespective of whether the LAI was below or above its critical value, providing experimental evidence that R/FR ratio is positively associated with pod initiation in soybean canopies. An increase in SPP produced a direct and steady increase in SN regardless of PN and plant density. A yield increase was observed for the L-LD treatment, which combined the increased SPP of L lines with the highest PN of L-LD canopies. These results have implications for crop management and breeding strategies aimed at increasing the yield potential of soybean.
To elucidate the mechanism by which intercropping proso millet (Panicum miliaceum L.) with mung bean (Vigna radiata L.) increases proso millet yield and to determine how this higher yield results from maximization of resources use efficiency, we designed and conducted four strip intercropping row arrangements, including two rows of proso millet alternating with two rows of mung bean (2P2M), four rows of proso millet alternating with two rows of mung bean (4P2M), four rows of proso millet alternating with four rows of mung bean (4P4M), two rows of proso millet alternating with four rows of mung bean (2P4M), sole proso millet (SP, control) and sole mung bean (SM, control) in Yulin, Shaanxi, China. Photosynthetically active radiation (PAR) in the canopy, radiation use efficiency (RUE), leaf photosynthetic characteristics, dry matter accumulation and allocation, and yield of proso millet were investigated. The results showed that the intercropping systems had higher PAR than the monoculture. Mean PAR intensities were increased by respectively 2.2%-23.4%, 19.8%-59.7%, and 61.2%-133.3% in the proso millet upper, middle and lower canopies compared with SP. The increase in PAR directly increased RUE, a result attributed mainly to the increase in photosynthetic capacity, including net photosynthetic rate and chlorophyll content. These responses resulted in increased dry matter allocation to plant organs. Yield of intercropped proso millet was 6.8%-37.3% higher than that under monoculture and the land equivalent ratios for the different intercropping patterns were all greater than unity (> 1). In general, yield followed a positive linear function of PAR in the intercropping system. The results indicated that intercropping can boost proso millet yield, evidently by altering light distribution within its canopy and consequently increasing RUE, thereby increasing leaf photosynthetic capacity, dry matter accumulation, and allocation to the grain. The optimum combination for improving the growth and yield of proso millet on the Loess Plateau of China was 2P4M.
