Foliar fungal diseases (rust and late leaf spot) incur large yield losses, in addition to the deterioration of fodder quality in groundnut worldwide. High oleic acid has emerged as a key market trait in groundnut, as it increases the shelf life of the produce/products in addition to providing health benefits to consumers. Marker-assisted backcrossing (MABC) is the most successful approach to introgressing or pyramiding one or more traits using trait-linked markers. We used MABC to improve three popular Indian cultivars (GJG 9, GG 20, and GJGHPS 1) for foliar disease resistance (FDR) and high oleic acid content. A total of 22 BC₃F₄ and 30 BC₂F₄ introgression lines (ILs) for FDR and 46 BC₃F₄ and 41 BC₂F₄ ILs for high oleic acid were developed. Recurrent parent genome analysis using the 58 K Axiom_Arachis array identified several lines showing upto 94% of genome recovery among second and third backcross progenies. Phenotyping of these ILs revealed FDR scores comparable to the resistant parent, GPBD 4, and ILs with high (~80%) oleic acid in addition to high genome recovery. These ILs provide further opportunities for pyramiding FDR and high oleic acid in all three genetic backgrounds as well as for conducting multi-location yield trials for further evaluation and release for cultivation in target regions of India.

Rice florets are subtended by two sterile lemmas, whose origin and biological functions have not been studied extensively. Here we demonstrate that two putative transcription factors, LAX PANICLE1 (LAX1) and FRIZZY PANICLE (FZP), synergistically control the development of sterile lemmas. Both LAX1 and FZP are previously known for their roles in panicle and floret development. Disruption of either LAX1 or FZP greatly reduces the number of floret development. We generated new lax1 mutants (lax1-c) using CRISPR/Cas9 gene editing technology. In addition to the expected lax panicle phenotypes, we noticed that a significant number of spikelets of lax1-c developed elongated sterile lemmas. Moreover, our characterization of lax1-RNAi plants also revealed sterile lemma phenotypes similar to lax1-c mutants. We isolated a weak allele of fzp (fzp-14) in a genetic screen for lax1-1 enhancers. The fzp-14 lax1-1 double mutants completely eliminated flower development. Interestingly, the isolated fzp-14 produced spikelets with elongated sterile lemmas. Furthermore, fzp-14 was haploid-insufficient in the lax1-1 background whereas fzp-14 heterozygous plants were indistinguishable from wild type plants. The lax1-1 fzp-14^+/− also developed elongated sterile lemma as observed in lax1-c, lax1-RNAi, and fzp-14, suggesting that LAX1 and FZP synergistically control sterile lemma development.

Higher amounts of cuticular wax in plants have been associated with improved plant stress tolerance and increased potential for industrial use. In this study, orthologs of KCS1 and CER1 in Arabidopsis, designated BnKCS1-1, BnKCS1-2, and BnCER1-2, were isolated from Brassica napus. Transcription of BnKCS1-1 and BnKCS1-2 in B. napus were induced by abscisic acid (ABA) and drought treatment, while transcription of BnCER1-2 was induced only by drought treatment. All three gene transcripts decreased significantly when plants were treated with methyl jasmonate (MeJA) or subjected to cold stress. Overexpression of BnKCS1-1, BnKCS1-2, and BnCER1-2 under the control of the CaMV35S promoter led to a significant increase in cuticular wax on transgenic B. napus leaves. BnKCS1-1 and BnKCS1-2 overexpression led to similar differences from non-transformed plants, with significantly higher levels of aldehydes (C₂₉ and C₃₀), alkanes (C₂₈, C₂₉, and C₃₁) and secondary alcohols (C₂₈ and C₂₉), and a significantly lower level of C₂₉ ketone. Overexpression of BnCER1-2 led to an increase in alkanes (C₂₇, C₂₈, C₂₉, and C₃₁), a decrease in secondary alcohols (C₂₈ and C₂₉), and insignificant changes in other wax components. Scanning electron microscopy revealed that overexpression of BnKCS1-1, BnKCS1-2, and BnCER1-2 in B. napus resulted in a higher density of wax crystals on the leaf surface than observed in non-transformed plants. Transgenic plants showed a reduced rate of water loss and increased drought tolerance compared to non-transformed plants. These results suggest that BnKCS1-1, BnKCS1-2, and BnCER1-2 gene products can modify the cuticular wax of B. napus. Changing cuticular waxes using transgenic approaches is a new strategy for genetic improvement of plant drought tolerance and provides an opportunity for development of B. napus as a surface-wax crop.

Nitrogen (N), a macronutrient essential for plant growth and development, is needed for biosynthesis of protein and starch, which affect grain yield and quality. Application of high-N fertilizer increases plant growth, grain yield, and flour quality. In this study, we performed the first comparative analysis of gliadin and glutenin subproteomes during kernel development in the elite Chinese wheat cultivar Zhongmai 175 under high-N conditions by reversed-phase ultra-performance liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE). Application of high-N fertilizer led to significant increases in gluten macropolymer content, total gliadin and glutenin content, and the accumulation of individual storage protein components. Of 126 differentially accumulated proteins (DAPs) induced by high-N conditions, 24 gliadins, 12 high-molecular-weight glutenins, and 27 low-molecular-weight glutenins were significantly upregulated. DAPs during five kernel developmental stages displayed multiple patterns of accumulation. In particular, gliadins and glutenins showed respectively five and six accumulation patterns. The accumulation of storage proteins under high-N conditions may lead to improved dough properties and bread quality.

The amylose content (AC) of rice endosperm starch varies from 0 to 35%, and is associated with rice cooking and eating quality. Soft rice has low AC, generally between 6% and 15%, and its eating quality is high whether it is consumed hot or cold. However, the appearance quality of current soft rice cultivars needs to be improved, especially opaque endosperm. Conventional genetic engineering has improved some agronomic traits of soft rice varieties, but not endosperm appearance. In the present study, a RNAi construct of the soluble starch synthase II-2 (SSSII-2) and the hygromycin phosphotransferase (HPT) gene were introduced into an elite japonica rice variety, Kangtiaowuyunjing (KWY8) by co-transformation. Several selectable marker-free (SMF) transgenic lines were obtained, and SSSII-2 expression was significantly downregulated in selected transgenic lines, resulting in lower AC of the endosperm. The physicochemical properties of the transgenic rice kernels, including gel consistency (GC) and rapid visco analyzer (RVA) profile, differed significantly from those of wild-type rice and were similar to those of a soft rice variety, Nanjing 46 (NJ46). These findings indicate that the cooking, eating, and processing qualities of transgenic rice are comparable to those of NJ46. However, the transgenic rice endosperm retained a transparent appearance under low-moisture conditions. Thus, SMF SSSII-2 RNAi rice provides a resource for breeding soft rice with transparent endosperm.

Short basal internodes are important for lodging resistance of rice (Oryza sativa L.). Several canopy indices affect the elongation of basal internodes, but uncertainty as to the key factors determining elongation of basal internodes persists. The objectives of this study were (1) to identify key factors affecting the elongation of basal internodes and (2) to establish a quantitative relationship between basal internode length and canopy indices. An inbred rice cultivar, Yinjingruanzhan, was grown in two split-plot field experiments with three N rates (0, 75, and 150 kg N ha⁻¹ in early season and 0, 90, and 180 kg N ha⁻¹ in late season) as main plots, three seedling densities (16.7, 75.0, and 187.5 seedlings m⁻²) as subplots, and three replications in the 2015 early and late seasons in Guangzhou, China. Light intensity at base of canopy (L_b), light quality as determined from red/far-red light ratio (R/FR), light transmission ratio (LTR), leaf area index (LAI), leaf N concentration (NLV) and final length of second internode (counted from soil surface upward) (FIL) were recorded. Higher N rate and seedling density resulted in significantly longer FIL. FIL was negatively correlated with L_b, LTR, and R/FR (P < 0.01) and positively correlated with LAI (P < 0.01), but not correlated with NLV (P > 0.05). Stepwise linear regression analysis showed that FIL was strongly associated with L_b and LAI (R² = 0.82). Heavy N application to pot-grown rice at the beginning of first internode elongation did not change FIL. We conclude that FIL is determined mainly by L_b and LAI at jointing stage. NLV has no direct effect on the elongation of basal internodes. N application indirectly affects FIL by changing LAI and light conditions in the rice canopy. Reducing LAI and improving canopy light transmission at jointing stage can shorten the basal internodes and increase the lodging resistance of rice.

The shape of an inflorescence varies among cereals, ranging from a highly branched panicle in rice to a much more compact spike in barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). However, little is known about the molecular basis of cereal inflorescence architecture. We profiled transcriptomes at three developmental stages of the barley main shoot apex — spikelet initiation, floral organ differentiation, and floral organ growth — and compared them with those from vegetative seedling tissue. Transcript analyses identified 3688 genes differentially transcribed between the three meristem stages, with a further 1394 genes preferentially expressed in reproductive compared with vegetative tissue. Co-expression assembly and Gene Ontology analysis classified these 4888 genes into 28 clusters, revealing distinct patterns for genes such as transcription factors, histone modification, and cell-cycle progression specific for each stage of inflorescence development. We also compared expression patterns of VRS (SIX-ROWED SPIKE) genes and auxin-, gibberellic acid- and cytokinin-associated genes between two-rowed and six-rowed barley to describe regulators of lateral spikelet fertility. Our findings reveal barley inflorescence phase-specific gene expression, identify new candidate genes that regulate barley meristem activities and flower development, and provide a new genetic resource for further dissection of the molecular mechanisms of spike development.

Accurate estimation of biomass is necessary for evaluating crop growth and predicting crop yield. Biomass is also a key trait in increasing grain yield by crop breeding. The aims of this study were (i) to identify the best vegetation indices for estimating maize biomass, (ii) to investigate the relationship between biomass and leaf area index (LAI) at several growth stages, and (iii) to evaluate a biomass model using measured vegetation indices or simulated vegetation indices of Sentinel 2A and LAI using a deep neural network (DNN) algorithm. The results showed that biomass was associated with all vegetation indices. The three-band water index (TBWI) was the best vegetation index for estimating biomass and the corresponding R²,²², RMSE, and RRMSE were 0.76, 2.84 t ha⁻¹, and 38.22% respectively. LAI was highly correlated with biomass (R² = 0.89, RMSE = 2.27 t ha⁻¹, and RRMSE = 30.55%). Estimated biomass based on 15 hyperspectral vegetation indices was in a high agreement with measured biomass using the DNN algorithm (R² = 0.83, RMSE = 1.96 t ha⁻¹, and RRMSE = 26.43%). Biomass estimation accuracy was further increased when LAI was combined with the 15 vegetation indices (R² = 0.91, RMSE = 1.49 t ha⁻¹, and RRMSE = 20.05%). Relationships between the hyperspectral vegetation indices and biomass differed from relationships between simulated Sentinel 2A vegetation indices and biomass. Biomass estimation from the hyperspectral vegetation indices was more accurate than that from the simulated Sentinel 2A vegetation indices (R² = 0.87, RMSE = 1.84 t ha⁻¹, and RRMSE = 24.76%). The DNN algorithm was effective in improving the estimation accuracy of biomass. It provides a guideline for estimating biomass of maize using remote sensing technology and the DNN algorithm in this region.

With increasing demand for high-quality cotton, it is desirable to identify genes involved in fiber development for molecular improvement of cotton. In this study, 780 differentially expressed genes (DEGs) were identified in developing fibers at 10 days post-anthesis (DPA) in Gossypium hirsutum acc. DH962 and G. hirsutum cv. Jimian 5 using RNA-seq. Of 15 stable QTL for fiber quality identified in the same two parents in previous studies, 4, 3, 6, 1, and 1 QTL were associated with fiber length (FL), fiber strength (FS), micronaire (MIC), fiber elongation (FE) and fiber length uniformity ratio (FU), respectively. Integration of DEGs and QTL allowed the identification of 31 genes in 9 QTL regions, of which 25 were highly expressed in fibers based on the transcriptome datasets and 9 were preferentially expressed in different stages of fiber development. Gh_A01G0453 (GhDTX19), Gh_D07G1581 and Gh_D04G0942 were expressed specifically in 5 and 10 DPA fibers, with Gh_D04G0942 showing low expression in other tissues except pistil. Gh_D07G1799 (GhGAUT9), Gh_D11G0326 (GhVPS29), Gh_D11G0333 (GhTCP14), and Gh_D11G0334 (GhNRP2) were preferentially expressed in 5 or 10 DPA fibers; Gh_A01G0397 (GhABCG10) and Gh_D07G1744 were expressed specifically in 20 and 25 DPA fibers. These results suggest candidate genes for molecular improvement of cotton fiber quality.

Identification and deployment of high-yielding and stress-tolerant maize hybrids adapted to stress-prone agro-ecologies is important for improving the food security and livelihoods of smallholder farmers in eastern Africa. The objectives of this study were to (i) assess the performance of maize hybrids under well-watered and drought stress conditions; (ii) evaluate grain yield stability of 65 intermediate-maturing and 55 early-maturing hybrids in 24 well-watered locations and seven drought stress locations; and (iii) identify representative and/or discriminative testing locations for increasing genetic gains for the target traits. There were significant differences for grain yield among early- and intermediate-maturing hybrids tested under well-watered and drought stress environments. Among the early-maturing hybrids, the top 10 hybrids produced 46.8%-73.9% and 31.2%-42.1% higher mean grain yields than the best commercial check under drought and well-watered conditions, respectively. Among the intermediate-maturing hybrids, the top 10 hybrids produced 25.2%-47.7% and 8.5%-13.5% higher grain yield than commercial checks under drought stress and well-watered conditions, respectively, suggesting improvement in the levels of drought tolerance in both early- and intermediate-maturing hybrids. GGE biplot analysis and a bi-segmented regression linear method identified specific early-maturing and intermediate-maturing hybrids that performed well under both well-watered and drought stress conditions. These hybrids could be recommended for commercial production in eastern Africa. Kakamega in Kenya was found to be the most representative and highly discriminating site among well-watered testing locations, while Kabuku in Tanzania was the least representative of test locations. For testing under drought stress conditions, Kiboko in Kenya was identified as the most representative location. This information could be useful for allocating resources and streamlining CIMMYT maize hybrid testing in eastern Africa.

The source-sink relationship determines the ultimate grain yield. We investigated the genetic basis of the relationship between source and sink and yield potential in rice. In two environments, we identified quantitative trait loci (QTL) associated with sink capacity (total spikelet number per panicle and thousand-grain weight), source leaf (flag leaf length, flag leaf width and flag leaf area), source-sink relationship (total spikelet number to flag leaf area ratio) and yield-related traits (filled grain number per panicle, panicle number per plant, grain yield per plant, biomass per plant, and harvest index) by genome-wide association analysis using 272 Xian (indica) accessions. The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations. A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers. Five QTL were detected consistently in four chromosomal regions in both environments. Five QTL clusters simultaneously affected source, sink, source-sink relationship, and grain yield traits, probably explaining the genetic basis of significant correlations of grain yield with source and sink traits. We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium (LD) blocks associated with significant SNPs and performing haplotype analysis. The genes included one cloned gene (NOG1) and three newly identified QTL (qHI6, qTGW7, and qFLA8). These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source-sink relationships using marker-assisted selection.

The cell wall composition and structure of the maize stalk directly affects its digestibility and in turn its feed value. Previous studies of stem quality have focused mostly on common maize germplasm, and few studies have focused on high-oil cultivars with high grain and straw quality. Investigation of the genetic basis of cell wall composition and digestibility of maize stalk using high-oil maize is desirable for improving maize forage quality. In the present study, a high-oil inbred line (By804) was crossed as male parent with the maize inbred line B73 to construct a population of 188 recombinant inbred lines (RILs). The phenotypes of six cell-wall-related traits were recorded, and QTL analysis was performed with a genetic map constructed with SNP markers. All traits were significantly correlated with one another and showed high broad-sense heritability. Of 20 QTLs mapped, the QTL associated with each trait explained 10.0%-41.1% of phenotypic variation. Approximately half of the QTL each explained over 10% of the phenotypic variation. These results provide a theoretical basis for improving maize forage quality by marker-assisted selection.

Optimized nitrogen (N) management can increase N-use efficiency in intercropping systems. Legume-nonlegume intercropping systems can reduce N input by exploiting biological N fixation by legumes. Measurement of N utilization can help in dissecting the mechanisms underlying N uptake and utilization in legume-nonlegume intercropping systems. An experiment was performed with three planting patterns: monoculture maize (MM), monoculture soybean (SS), and maize-soybean relay intercropping (IMS), and three N application levels: zero N (NN), reduced N (RN), and conventional N (CN) to investigate crop N uptake and utilization characteristics. N recovery efficiency and ¹⁵N recovery rate of crops were higher under RN than under CN, and those under RN were higher under intercropping than under the corresponding monocultures. Compared with MM, IMS showed a lower soil N-dependent rate (SNDR) in 2012. However, the SNDR of MM rapidly declined from 86.8% in 2012 to 49.4% in 2014, whereas that of IMS declined slowly from 75.4% in 2012 to 69.4% in 2014. The interspecific N competition rate (NCR_ms) was higher under RN than under CN, and increased yearly. Soybean nodule dry weight and nitrogenase activities were respectively 34.2% and 12.5% higher under intercropping than in monoculture at the beginning seed stage. The amount (Ndfa) and ratio (%Ndfa) of soybean N₂ fixation were significantly greater under IS than under SS. In conclusion, N fertilizer was more efficiently used under RN than under CN; in particular, the relay intercropping system promoted N fertilizer utilization in comparison with the corresponding monocultures. An intercropping system helps to maintain soil fertility because interspecific N competition promotes biological N fixation by soybean by reducing N input. Thus, a maize-soybean relay intercropping system with reduced N application is sustainable and environmentally friendly.

Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae) is a common maize disease that not only severely reduces grain yield but also contaminates maize grain with mycotoxins. We investigated the molecular mechanism underlying the host defense responses against pathogen infection using comparative transcriptomic analysis. We injected F. graminearum spore suspensions into plants of resistant (IBM-81) and a susceptible (IBM-85) maize inbred line after pollination and performed RNA-seq 48, 72, and 96 h after inoculation. Respectively 487 and 410 differentially expressed genes (DEGs) were induced in the resistant and susceptible lines across three time points, indicating that a stronger defense response was activated in the resistant than in the susceptible line. Among them, 198 genes commonly induced in the two lines were subjected to pathway analysis, revealing that most of the DEGs were closely associated with defense and a wide range of metabolic activities. DEGs associated with pathogenesis-related protein 1 (PR1) and regulation of salicylic acid were significantly enriched during F. graminearum infection, suggesting that these DEGs play dominant roles in maize resistance to GER. Our results provide a resource for future gene discovery and facilitate elucidation of the complex defense mechanisms involved in resistance to GER.

This study was aimed at developing a protocol for increasing the number of generation cycles per year in chickpea (Cicer arietinum L.). Six accessions, two each from early (JG 11 and JG 14), medium (ICCV 10 and JG 16), and late (CDC-Frontier and C 235) maturity groups, were used. The experiment was conducted for two years under glasshouse conditions. The photoperiod was extended to induce early flowering and immature seeds were germinated to further reduce generation cycle time. Compared to control, artificial light caused a reduction in flowering time by respectively 8-19, 7-16, and 11-27 days in early-, medium-, and late-maturing accessions. The earliest stage of immature seed able to germinate was 20-23 days after anthesis in accessions of different maturity groups. The time period between germination and the earliest stage of immature seed suitable for germination was considered one generation cycle and spanned respectively 43-60, 44-64, and 52-79 days in early-, medium-, and late-maturing accessions. However, the late-maturing accession CDC-Frontier could not be advanced further after three generation cycles owing to the strong influence of photoperiod and temperature. The mean total number of generations produced per year were respectively 7, 6.2, and 6 in early-, medium-, and late-maturing accessions. These results have encouraging implications for breeding programs: rapid progression toward homozygosity, development of mapping populations, and reduction in time, space and resources in cultivar development (speed breeding).