Sugar metabolism plays an essential role in plant male reproduction. Defects in sugar metabolism during anther and pollen development often result in genic male sterility (GMS). In this review, we summarize the recent progresses of the sugar metabolism-related GMS genes and their roles during plant anther and pollen development, including callose wall and primexine formation, intine development, pollen maturation and starch accumulation, anther dehiscence, and pollen germination and tube growth. We predict 112 putative sugar metabolic GMS genes in maize based on bioinformatics and RNA-seq analyses, and most of them have peak expression patterns during middle or late anther developmental stages. Finally, we outline the potential applications of sugar metabolic GMS genes in crop hybrid breeding and seed production. This review will deepen our understanding on sugar metabolic pathways in controlling pollen development and male fertility in plants.

Normal microsporogenesis is determined by both nuclear and mitochondrial genes. In maize C-type cytoplasmic male sterility, it is unclear how the development of meiocytes and microspores is affected by the mitochondrial sterility gene and the nuclear restorer gene. In this study, we sequenced the transcriptomes of single meiocytes (tetrad stage) and early mononucleate microspores from sterile and restorer lines. The numbers of expressed genes varied in individual cells and fewer than half of the expressed genes were common to the same cell types. Four comparisons revealed 3379 differentially expressed genes (DEGs), with 277 putatively associated with mitochondria, 226 encoding transcription factors, and 467 possibly targeted by RF4. KEGG analysis indicated that the DEGs in the two lines at the tetrad stage were involved predominantly in carbon metabolism and in amino acid biosynthesis and metabolism, whereas the DEGs during the transition from the tetrad stage to the early mononucleate stage were associated mostly with regulation of protein metabolism, fatty acid metabolism, and anatomical structure morphogenesis. Thus, meiocyte and microspore development was affected by the surrounding cells and the restorer gene, and the restorer gene helped restore the redox homeostasis of microspores and the normal cellular reconstruction during the transition.

Anther development is a programmed biological process crucial to plant male reproduction. Genome-wide analyses on the functions of transcriptional factor (TF) genes and their microRNA (miRNA) regulators contributing to anther development have not been comprehensively performed in maize. Here, using published RNA-Seq and small RNA-Seq (sRNA-Seq) data from maize anthers at ten developmental stages in three genic male-sterility (GMS) mutants (ocl4, mac1, and ms23) and wild type W23, as well as newly sequenced maize anther transcriptomes of ms7-6007 and lob30 GMS mutants and their WT lines, we analyzed and found 1079 stage-differentially expressed (stage-DE) TF genes that can be grouped into six (premeiotic, meiotic, postmeiotic, premeiotic-meiotic, premeiotic-postmeiotic, and meiotic-postmeiotic clusters) expression clusters. Functional enrichment combined with cytological and physiological analyses revealed specific functions of genes in each expression cluster. In addition, 118 stage-DE miRNAs and 99 miRNA-TF gene pairs were identified in maize anthers. Further analyses revealed the regulatory roles of zma-miR319 and zma-miR159 as well as ZmMs7 and ZmLOB30 on ZmGAMYB expression. Moreover, ZmGAMYB and its paralog ZmGAMYB-2 were demonstrated as novel maize GMS genes by CRISPR/Cas9 knockout analysis. These results extend our understanding on the functions of miRNA-TF gene regulatory pairs and GMS TF genes contributing to male fertility in plants.

Genic male sterility (GMS) is one of the most important resources for exploiting heterosis in crop breeding, so that identifying genomic loci regulating GMS is desirable. However, many regulatory genes controlling GMS have not yet been characterized in maize, owing partly to a lack of genetic materials. We generated a recessive male-sterile maize mutant in the Jing 724 genetic background via ethyl methanesulfonate treatment, and found the male sterility to be due to a single gene mutation. Bulk-segregant RNA sequencing of three replicates indicated that one genomic region located at the end of chromosome 4 was associated with the observed mutant phenotype. Among genes with nonsynonymous mutations, Zm00001d053895 (bHLH51) showed abolished expression in the sterile bulks and was annotated as a bHLH transcription factor orthologous to Arabidopsis AMS, suggesting an association with the male sterility of the mutant. Kompetitive Allele-Specific PCR assays further validated the exclusive correlation of male sterility with the single C-to-T mutation in the fifth exon. The new maize mutant and the potential SNP locus provide novel genetic material for investigating the molecular mechanism underlying tapetal development and may facilitate the improvement of hybrid production systems.

Soybean [Glycine max (L.) Merr.] provides a rich source of plant protein and oil worldwide. The commercial use of transgenic technology in soybean has become a classical example of the application of biotechnology to crop improvement. Although genetically modified soybeans have achieved commercial success, hybrid soybean breeding is also a potential way to increase soybean yield. Soybean cytoplasmic male-sterile (CMS) lines have been used in three-line hybrid breeding systems, but their application to exploiting soybean heterosis has been limited by rare germplasm resource of sterile lines. The generation of various genetic diversity male-sterile soybean lines will help to overcome the shortcoming. In this study, we used targeted editing of AMS homologs in soybean by CRISPR/Cas9 technology for the first time to generate stable male-sterile lines. Targeted editing of GmAMS1 resulted in a male-sterile phenotype, while editing of GmAMS2 failed to produce male-sterile lines. GmAMS1 functions not only in the formation of the pollen wall but also in the controlling the degradation of the soybean tapetum. CRISPR/Cas9 technology could be used to rapidly produce stable male-sterile lines, providing new sterile-line materials for soybean hybrid breeding systems.

In plants, non-green plastids in heterotrophic tissues are sites for starch and fatty acids biosynthesis, which are essential for plant development and reproduction. Distinct from chloroplasts, the metabolites for these processes in non-green plastids have to be imported through specific transporters. Glucose 6-Phosphate/Phosphate Translocator 1 is required for the uptake of cytosolic Glucose 6-Phosphate into non-green plastids. In Arabidopsis, GPT1 has been demonstrated to play essential roles in male, female gametophyte and embryo development. However, the roles of GPTs in other species are yet largely unknown. Here, we reported that rice OsGPT1 is indispensable for normal tapetal degeneration and pollen exine formation during anther and pollen development. OsGPT1 is localized in the plastid and distributed in the anther wall layers and late-stage pollen grains. Different from the gametic defects caused by mutation in AtGPT1, disruption of OsGPT1 does not affect male and female gamete transmission as well as embryo development. On the contrary, osgpt1 mutant exhibits delayed tapetum degeneration, decreased Ubisch bodies formation and thinner pollen exine, leading to pollen abortion at the mature stage. Furthermore, the expression of several genes involved in tapetal programmed cell death (PCD) and sporopollenin formation is decreased in osgpt1. Our study suggests that OsGPT1 coordinates the development of anther sporophytic tissues and the male gametophyte by integrating carbohydrate and fatty acid metabolism in the plastid.

TaMs1 encodes a non-specific lipid transfer protein (nsLTP) and is required for pollen development in wheat. Although MS1 is a Poaceae-specific gene, the roles of MS1 genes in other Poaceae plants are unknown, especially in rice and maize. Here, we identified one ortholog in rice (OsLTPg29) and two orthologs in maize (ZmLTPg11 and ZmLTPx2). Similar to TaMs1, both OsLTPg29 and ZmLTPg11 genes are specifically expressed in the microsporocytes, and both OsLTPg29 and ZmLTPg11 proteins showed lipid-binding ability to phosphatidic acid and several phosphoinositides. To determine their roles in pollen development, we created osltpg29 mutants and zmltpg11zmltpx2 double mutants by CRISPR/Cas9. osltpg29, not zmltpg11zmltpx2, is defective in pollen development, and only OsLTPg29, not ZmLTPg11, can rescue the male sterility of tams1 mutant. Our results demonstrate that the biological function of MS1 in pollen development differs in the evolution of Poaceae plants.

The anther cuticle and pollen exine play a critical role in male gametophyte development. The sporopollenin precursors and cuticular lipid monomers are transported to the surface of the microspores and the epidermis by lipid transport proteins (LTPs) and ATP-binding cassette G (ABCG) transporters for the formation of the pollen wall and anther cuticle, respectively. However, the function of ABCG transporters in maize anther development is unclear. Here, we cloned the MS2 gene from the maize male sterile2 mutant using map-based cloning and determined that it encodes an ABCG transporter. MS2 protein was experimentally confirmed to be located on the cell membrane. The quantitative real-time PCR (qRT-PCR) results showed that MS2 was ubiquitously expressed in all vegetative and reproductive tissues, whereas a high transcriptional level of MS2 was observed in anthers, especially at the young microspore stage. Gas chromatography-mass spectrometry (GC-MS) analysis showed decreased accumulation of cutin and wax components in ms2 anthers, indicating that MS2 plays a role in the transport of lipid molecules to anther cuticle and pollen exine. To our knowledge, MS2 is the first reported ABCG transporter gene that participates in anther development in maize.

Male sterility is a common biological phenomenon in plant kingdom and has been used to generate male-sterile lines, which are important genetic resources for commercial hybrid seed production. Although increasing numbers of male-sterility genes have been identified in rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), few male-sterility-related genes have been characterized in foxtail millet (Setaria italica). In this study, we isolated a male-sterile ethyl methanesulfonate-generated mutant in foxtail millet, no pollen 1 (sinp1), which displayed abnormal Ubisch bodies, defective pollen exine and complete male sterility. Using bulk segregation analysis, we cloned SiNP1 and confirmed its function with CRISPR/Cas9 genome editing. SiNP1 encoded a putative glucose-methanol-choline oxidoreductase. Subcellular localization showed that the SiNP1 protein was preferentially localized to the endoplasmic reticulum and was predominantly expressed in panicle. Transcriptome analysis revealed that many genes were differentially expressed in the sinp1 mutant, some of which encoded proteins putatively involved in carbohydrate metabolism, fatty acid biosynthesis, and lipid transport and metabolism, which were closely associated with pollen wall development. Metabolome analysis revealed the disturbance of flavonoids metabolism and fatty acid biosynthesis in the mutant. In conclusion, identification of SiNP1 provides a candidate male-sterility gene for heterosis utilization in foxtail millet and gives further insight into the mechanism of pollen reproduction in plants.

The Nsa cytoplasmic male sterility (CMS) system confers stable male sterility and offers great potential for production of hybrid seeds in oilseed rape. However, genes responsible for male sterility in Nsa CMS have not been identified. By mitochondrial genome sequencing of Nsa CMS and its maintainer line, we identified in an Nsa CMS line several chimeric genes encoding hypothetical proteins harboring transmembrane domains. One novel chimeric gene orf346 showed high identity with cox1 at the 5′ terminal region and was co-transcribed with nad3 and rps12 genes. Transgenic plants of orf346 fused with or without mitochondrial targeting peptide conferred complete male sterility in Arabidopsis. ORF346 was mitochondrion-localized. Expression of orf346 in Escherichia coli inhibited bacterial growth, with excessive accumulation of reactive oxygen species and decreased ATP content. These results reveal a link between the newly identified mitochondrial gene orf346 and the abortion of Nsa CMS. Inadequate energy supply and excessive accumulation of reactive oxygen species may account for pollen abortion in Nsa CMS plants.

A nuclear-encoded sigma (σ) factor is essential for the transcriptional regulation of plant chloroplast-encoded genes. Five putative maize σ factors have been identified by database searches, but their functions are unknown. We report a maize leaf color mutant etiolated/albino leaf 1 (eal1) that was derived from space mutation breeding. The eal1 mutant displays etiolated or albino leaves that then gradually turn to normal green at the seedling stage. The changes in eal1 leaf color are associated with changes in photosynthetic pigment content and chloroplast development. Map-based cloning revealed that a single amino-acid deletion changing Val₄₈₀-Val₄₈₁-Val₄₈₂ to Val₄₈₀-Val₄₈₁, in the C-terminal domain σ₄ of the putative σ factor ZmSig2A, is responsible for the eal1 mutation. In comparison with the expression level of the wild-type (WT) allele ZmSig2A⁺ in WT plants, much higher expression of the mutant allele ZmSig2A^ΔV in eal1 plants was detected before the eal1 plants turned to normal green. ZmSig2A shows the highest similarity to rice OsSig2A and Arabidopsis SIG2. Ectopic expression of ZmSig2A⁺ or ZmSig2A^ΔV driven by the cauliflower mosaic virus 35S promoter rescued the pale green leaf of the sig2 mutant, but ectopic expression of ZmSig2A^ΔV driven by the SIG2 promoter did not. We propose that the Val deletion generated a new weak allele of ZmSig2A that cannot completely abolish the ZmSig2A function. Some genes involved in chloroplast development and photosynthesis-associated nuclear genes showed significant expression differences between eal1 and WT plants. We conclude that ZmSig2A encoding a σ factor is essential for maize chloroplast development. The eal1 mutant with a weak allele of ZmSig2A represents a valuable genetic resource for investigating the regulation of ZmSig2A-mediated chloroplast development in maize. The eal1 mutation may be useful as a marker for early identification and elimination of false hybrids or transgene transmission in the application of genetic male sterility to commercial hybrid seed production.

In rice, high-temperature stress (HT) during flowering results in decreased grain yield via a reduction in spikelet fertility; however, the effect of plant water status on spikelet fertility under HT remains unknown. To investigate the relationship between spikelet water status and spikelet fertility under HT, two experiments were performed under temperature-controlled conditions using four genotypes with varying tolerance to HT. Rice plants were exposed to HT for seven consecutive days during the flowering stage under three soil water treatments (soil water potential 0, −20, and −40 kPa), as well as under hydroponic conditions in a separate experiment. HT significantly decreased spikelet fertility, pollen fertility, and anther dehiscence under each of the three water treatments. HT significantly increased the spikelet transpiration rate, and this change was accompanied by a significant decrease in the internal temperature of the spikelets. HT decreased pollen grain diameter in heat-sensitive genotypes. HT had varying effects on the water potential of panicles and anthers but increased anther soluble-sugar concentration. Different aquaporin genes showed different expression profiles under HT, and the expression levels of PIPs for plasma membrane intrinsic proteins and TIPs for tonoplast intrinsic proteins increased in anthers but decreased in glumes. Correlation analyses showed that anther dehiscence and pollen (spikelet) fertility were tightly associated with anther water status, and the expression levels of almost all anther aquaporin genes were significantly correlated with anther dehiscence under HT. In summary, an increased spikelet transpiration rate and decreased internal spikelet temperature were associated with alleviation of the effects of HT in rice genotypes with varying degrees of heat tolerance, and the response of spikelet water status to HT, involving increased total expression of aquaporins and soluble sugar content, thereby improved pollen fertility, anther dehiscence, and spikelet fertility, especially in heat-resistant genotypes. The heat-resistant genotypes N22 and SY63 may adopt different approaches to reduce heat damage.

Wheat leaf rust is a prevalent foliar disease in wheat worldwide. Growing resistant cultivars is an effective strategy to minimize the impact of leaf rust on yield and grain quality. Lr42 is a leaf rust resistance gene identified from Aegilops tauschii and is still effective against current predominant leaf rust races in the United States and many other countries. In this study, we developed diagnostic DNA markers for Lr42 using the sequence polymorphisms of a differentially expressed gene (TaRPM1) encoding a putative NB-ARC protein in the Lr42 candidate region identified by RNA-sequencing of two near-isogenic lines contrasting in Lr42 alleles. Markers were designed based on a deletion mutation and a single nucleotide polymorphism (SNP) in the gene. Haplotype analyses of the newly developed markers in the three diversity panels demonstrated that they are diagnostic for Lr42, and superior to previously used markers in selection accuracy. These markers have the advantages of low cost and easy assay, and they are suitable for marker-assisted selection in breeding programs with either high- or low-throughput marker screening facilities.

Simple sequence repeat (SSR) markers have been proved to be a very powerful tool for quantitative trait locus (QTL) mapping, marker-assisted selection and comparative genomics research in many crop species. However, a high-density SSR genetic linkage map is still lacking because there are only a few SSR markers available in sweet potato. In this study, a total of 2545 simple sequence repeat (SSR) primer pairs, including 1215 genomic SSR (gSSR) primer pairs and 1330 BES-SSR (bSSR) primer pairs designed from the genome sequence and BAC-end sequence of sweet potato, respectively, were screened with sweet potato cultivars Luoxushu 8 and Zhengshu 20 and their randomly sampled two F₁ individuals and 571 of them generated polymorphic bands. The selected 571 polymorphic SSR primer pairs and 35 EST-based SSR (eSSR) primer pairs developed at our laboratory were used to genotype 240 F₁ individuals derived from a cross between Luoxushu 8 and Zhengshu 20. A double pseudo-test-cross strategy was applied for linkage analysis. The Luoxushu 8 map included 90 linkage groups with 5057 SSR markers and covered 13,299.9 cM with a marker density of 2.6 cM, and the Zhengshu 20 map contained 90 linkage groups with 3009 SSR markers and covered 11,122.9 cM with a marker density of 3.7 cM. Fifteen homologous groups were identified in both parent maps. These are the first SSR linkage maps consisting of the complete 90 linkage groups and 15 homologous groups, which are consistent with the autohexaploid nature of sweetpotato, and are also the linkage maps with the highest SSR marker density reported to date. These results provide a basis for QTL mapping, marker-assisted breeding and comparative genomics research of sweet potato.

Poor filling and low weight of inferior kernels limit the further improvement of wheat yield. Two cultivars, Shuangda 1 and Xinong 538, with different grain weights, were selected to investigate the physiological changes of inferior kernels by removal of superior kernels (RS) at the flowering stage. iTRAQ combined with physiological indexes was used to identify factors limiting the filling of inferior kernels. Removal of superior kernels significantly increased the mean filling rate of inferior kernels and thus increased their weight. A set of 6012 proteins in inferior wheat kernels were differentially expressed between the RS and control. These differentially expressed proteins were involved mainly in carbon metabolism and energy metabolism. The main reason for the promoting effect of RS on the filling of inferior kernels may be that RS downregulated proteins involved in glycolysis and pyruvate metabolism while upregulating proteins involved in carbon fixation and photosynthesis. Consequently, RS greatly increased the ATP content in inferior kernels, supplying energy for them to absorb photosynthetic assimilates. Removal of superior kernels increased the activities of sucrose synthase, soluble starch synthase, adenosine diphosphate glucose pyrophosphorylase, and starch branching enzyme in inferior kernels and promoted starch accumulation in them. Thus, RS promoted the filling of inferior kernels and increased their weight. The promoting effect of RS on starch synthesis in inferior kernels was associated with their endogenous IAA and ABA levels.

Deep placement of nitrogen fertilizer is a key strategy for improving nitrogen use efficiency. A two-year field experiment was conducted during the early rice growing seasons (March-July) of 2016 and 2017. The experimental treatments comprised two rice cultivars: Wufengyou 615 (WFY 615) and Yuxiangyouzhan (YXYZ), and three N treatments: mechanical deep placement of all fertilizers as basal dose at 10 cm soil depth (one-time deep-placement fertilization, namely OTDP fertilization); manual surface broadcast (the common farmer practice) of 40% N fertilizer at one day before sowing (basal fertilizer) followed by broadcast application of 30% each at tillering and panicle initiation stages; and no fertilizer application at any growth stage as a control. One-time deep-placement fertilization increased grain yield of both rice cultivars by 11.8%-19.6%, total nitrogen accumulation by 10.3%-13.1%, nitrogen grain production efficiency by 29.7%-31.5%, nitrogen harvest index by 27.8%-30.0%, nitrogen agronomic efficiency by 71.3%-77.2%, and nitrogen recovery efficiency by 42.4%-56.7% for both rice cultivars, compared with the multiple-broadcast treatment. One-time deep-placement fertilization reduced CH₄-induced global warming potential (GWP) by 20.7%-25.3%, N₂O-induced GWP by 7.2%-12.3%, and total GWP by 14.7%-22.9% for both rice cultivars relative to the multiple-broadcast treatment. The activities of glutamine synthetase and nitrate reductase were increased at both panicle-initiation and heading stages in both rice cultivars following one-time deep-placement fertilization treatment. Larger leaf area index at heading stage and more favorable root morphological traits expressed as larger total root length, mean root diameter, and total root volume per hill were also observed. One-time deep-placement fertilization could be an effective strategy for increasing grain yield and nitrogen use efficiency and lowering greenhouse-gas emissions under mechanical direct-seeded cropping systems.

Increased grain yield (GY) and grain protein concentration (GPC) are the two main targets of efforts to improve wheat (Triticum aestivum L.) production in the North China Plain (NCP). We conducted a three-year field experiment in the 2014-2017 winter wheat growing seasons to compare the effects of conventional irrigation practice (CI) and micro-sprinkling irrigation combined with nitrogen (N) fertilizer (MSI) on GY, GPC, and protein yield (PY). Across the three years, GY, GPC, and PY increased by 10.5%-16.7%, 5.4%-8.0%, and 18.8%-24.6%, respectively, under MSI relative to CI. The higher GY under MSI was due primarily to increased thousand-kernel weight (TKW). The chlorophyll content of leaves was higher under MSI during the mid-late grain filling period, increasing the contribution of post-anthesis dry matter accumulation to GY, with consequent increases in total dry matter accumulation and harvest index compared to CI. During the mid-late grain filling period, the canopy temperature was markedly lower and the relative humidity was higher under MSI than under CI. The duration and rate of filling during the mid-late grain filling period were also higher under MSI than CI, resulting in higher TKW. MSI increased the contribution of post-anthesis N accumulation to grain N but reduced the pre-anthesis remobilization of N in leaves, the primary site of photosynthetic activity, possibly helping maintain photosynthate production in leaves during grain filling. Total N at maturity was higher under MSI than CI, although there was little difference in N harvest index. The higher GPC under MSI than under CI was due to a larger increase in grain N accumulation than in GY. Overall, MSI simultaneously increased both GY and GPC in winter wheat grown in the NCP.

Lodging is a major problem limiting maize yield worldwide. However, the mechanisms of lodging resistance remain incompletely understood for maize. Here, we evaluated 443 maize accessions for lodging resistance in the field. Five lodging-resistant accessions and five lodging-sensitive accessions were selected for further research. The leaf number, plant height, stem diameter, and rind penetrometer resistance were similar between lodging-resistant and -sensitive inbred lines. The average thickness of sclerenchymatous hypodermis layer was thicker and the vascular area was larger in the lodging-resistant lines compared with lodging-sensitive lines. Although total lignin content in stem tissue did not significantly differ between lodging-resistant and -sensitive lines, phloroglucinol staining revealed that the lignin content of the cell wall in the stem cortex and in the stem vascular tissue near the cortex was higher in the lodging-resistant lines than in the lodging-sensitive lines. Analysis of strand-specific RNA-seq transcriptome showed that a total of 793 genes were up-regulated and 713 genes were down-regulated in lodging-resistant lines relative to lodging-sensitive lines. The up-regulated genes in lodging-resistant lines were enriched in cell wall biogenesis. These results indicated that modification of cell wall biosynthesis would contribute to lodging resistance of maize.

Erratic rainfall and misalignment between the rainy season and the growing season of winter wheat greatly limit rainfed winter wheat yield in the Loess Plateau of China. To increase the grain yield of winter wheat in this region, the effects of different agronomic practices, including adjusting planting pattern (NR, narrow row spacing), increasing seeding rate (high seeding rate, HS), decreasing basal nitrogen rate and increasing top-dressed nitrogen rate (DBN), and replacing an old cultivar with a new cultivar (NC) on wheat yield were investigated for two consecutive years. The results showed that the current grain yield of rainfed winter wheat in the Loess Plateau could be increased to 5879-7093 kg ha⁻¹ by HS, DBN and NC practices relative to the practice of high-yielding farmers (PF). The increased yield due to HS, DBN and NC was attributed to the higher number of spikes ha⁻¹, 1000-grain weight, and kernels spike⁻¹. Before the flowering stage, HS increased soil water consumption (SWC) in 1-3 m subsoil due to the higher plant population compared with that of PF, whereas DBN decreased SWC in the 0-2 m soil layer compared with that of PF. After the flowering stage, HS, DBN, and NC increased SWC by 8-16 mm in 2-3 m subsoil compared to PF. The water use efficiency (WUE) was increased under DBN and NC in comparison with PF. However, the WUE did not increase under HS as it had the highest evapotranspiration among the five treatments. Increasing the use of subsoil water during the late growth stage by optimizing agronomic practices or applying new cultivars with expansive roots should be the primary approach to increase rainfed winter wheat yield in this region.

Bulked-segregant analysis is a time- and cost-saving strategy for identifying major quantitative trait loci (QTL) in a mapping population. Bulked-segregant analysis combined with whole-genome sequencing (BSA-seq) was performed to rapidly identify QTL for heading date, plant height, and panicle length in a large F₂ population derived from two landraces: Chuan 7 (C7) and Haoboka (HBK). Twenty plants with extremely low or high phenotypic values for the target traits were selected from an F₂ population of 940 plants to construct low- and high-value bulks. Three pairs of bulks for the three traits were constructed, resulting in six DNA pools. BSA-seq revealed nine QTL: four for heading date, three for plant height, and two for panicle length. These QTL were validated in a random F₂ population or BC₄F₂ populations. The major novel plant height QTL, qPH8, acting additively with an effect equivalent to that of semi-dwarf 1 (sd1), is potentially valuable for hybrid rice breeding. qPH8 controls mainly the elongation of basal internodes. The C7 allele of qPH8 reduces plant height and increases lodging resistance without yield penalty, suggesting a potential role for qPH8 in improving rice plant architecture.

Erratic rainfall often results in intermittent drought and/or waterlogging and limits maize (Zea mays L.) productivity in many parts of the Asian tropics. Developing climate-resilient maize germplasm possessing tolerance to these key abiotic stresses without a yield penalty under optimal growing conditions is a challenge for breeders working in stress-vulnerable agro-ecologies in the region. Breeding stress-resilient maize for rainfed stress-prone ecologies is identified as one of the priority areas for CIMMYT-Asia maize program. We applied rapid cycle genomic selection (RCGS) on two multiparent yellow synthetic populations (MYS-1 and MYS-2) to improve grain yield simultaneously under drought and waterlogging conditions using genomic-estimated breeding values (GEBVs). Also, the populations were simultaneously advanced using recurrent phenotypic selection (PS) by exposing them to managed drought and waterlogging and intermating tolerant plants from the two selection environments. Selection cycles per se (C₁, C₂, and C₃) of the two populations developed using RCGS and PS approach and their test-cross progenies were evaluated separately in multilocation trials under managed drought, waterlogging, and optimal moisture conditions. Significant genetic gains were observed with both GS and PS, except with PS in MYS-2 under drought and with GS in MYS-1 under waterlogging. Realized genetic gains from GS were relatively higher under drought conditions (110 and 135 kg ha⁻¹ year⁻¹) compared to waterlogging (38 and 113 kg ha⁻¹ year⁻¹) in both MYS-1 and MYS-2, respectively. However, under waterlogging stress PS showed at par or better than GS as gain per year with PS was 80 and 90 kg ha⁻¹, whereas with GS it was 90 and 43 kg ha⁻¹ for MYS-1 and MYS-2, respectively. Our findings suggested that careful constitution of a multiparent population by involving trait donors for targeted stresses, along with elite high-yielding parents from diverse genetic background, and its improvement using RCGS is an effective breeding approach to build multiple stress tolerance without compromising yield when tested under optimal conditions

Zhongshuang 11 (ZS11) is an elite inbred rapeseed (Brassica napus L.) cultivar widely planted in the Yangtze River basin for its favorable characteristics including high seed oil content (SOC), low seed glucosinolate content (SGC), long siliques, and stable yield. To transfer the ideal traits from ZS11 into 195-14A, a Polima (pol)-type cytoplasmic male sterile line with high general combining ability, a doubled haploid population derived from the cross of ZS11 and 195-14A was developed. Based on this population, a high-density genetic linkage map covering 2553 cM with an average marker interval of 0.81 cM, was constructed using the Brassica 60K SNP array and simple sequence repeats. In seven environments, 64, 29, 35, 37, and 33 QTL were identified for silique length, seeds per silique, seed density per silique, SOC, and SGC, respectively. Most favorable alleles were from ZS11. Seventy-one consensus QTL were identified by a QTL meta-analysis, eight of which (cqSL-A9-2, cqSL-C7, cqSGC-C2, cqSOC-A5-2, cqSOC-A5-3, cqSPS-A6-2, cqSPS-A7-2, and cqSDPS-A9-2) were assigned as major QTL. Comparative genomics and expression analysis predicted 72 candidate genes underlying the 21 consensus QTL for the five traits. These findings suggest the genetic basis of the superior performance of ZS11 and suggest favorable alleles for development of cultivars with improved yield and quality. These results will assist in cloning these promising alleles in the future.

Intercropping of maize (Zea mays L.) and peanut (Arachis hypogaea L.) often results in greater yields than the respective sole crops. However, there is limited knowledge of aboveground and belowground interspecific interactions between maize and peanut in field. A two-year field experiment was conducted to investigate the effects of interspecific interactions on plant growth and grain yield for a peanut/maize intercropping system under different nitrogen (N) and phosphorus (P) levels. The method of root separation was employed to differentiate belowground from aboveground interspecific interactions. We observed that the global interspecific interaction effect on the shoot biomass of the intercropping system decreased with the coexistence period, and belowground interaction contributed more than aboveground interaction to advantages of the intercropping in terms of shoot biomass and grain yield. There was a positive effect from aboveground and belowground interspecific interactions on crop plant growth in the intercropping system, except that aboveground interaction had a negative effect on peanut during the late coexistence period. The advantage of intercropping on grain came mainly from increased maize yield (means 95%) due to aboveground interspecific competition for light and belowground interaction (61%-72% vs. 28%-39% in fertilizer treatments). There was a negative effect on grain yield from aboveground interaction for peanut, but belowground interspecific interaction positively affected peanut grain yield. The supply of N, P, or N + P increased grain yield of intercropped maize and the contribution from aboveground interspecific interaction. Our study suggests that the advantages of peanut/maize intercropping for yield mainly comes from aboveground interspecific competition for maize and belowground interspecific facilitation for peanut, and their respective yield can be enhanced by N and P. These findings are important for managing the intercropping system and optimizing the benefits from using this system.

Appearance and cooked rice elongation are key quality traits of rice. Although some QTL for these traits have been identified, understanding of the genetic relationship between them remains limited. In the present study, large phenotypic variation was observed in 760 accessions from the 3K Rice Genomes Project for both appearance quality and cooked rice elongation. Most component traits of appearance quality and cooked rice elongation showed significant pairwise correlations, but a low correlation was found between appearance quality and cooked rice elongation. A genome-wide association study identified 74 QTL distributed on all 12 chromosomes for grain length, grain width, length to width ratio, degree of endosperm with chalkiness, rice elongation difference, and elongation index. Thirteen regions containing QTL stably expressed in multiple environments and/or exerting pleiotropic effects on multiple traits were detected. By gene-based association analysis and haplotype analysis, 46 candidate genes, including five cloned genes, and 49 favorable alleles were identified for these 13 QTL. The effect of the candidate gene Wx on rice elongation difference was validated by a transgenic strategy. These results shed light on the genetic bases of appearance quality and cooked rice elongation and provide gene resources for improving rice quality by molecular breeding.

Grain size is one of the most important agronomic traits controlling grain yield. Development of novel germplasm with large grains would be beneficial for crop improvement. We report the genetic identification and functional analysis of the LONG GRAIN 6 (LOG6) gene, which is identical to MITOGEN-ACTIVATED PROTEIN KINASE 6 (OsMAPK6), affecting grain length of rice. Map-based cloning revealed that the long-grain phenotype of log6-D results from a glutamine (E) to lysine (K) mutation in the conserved TEY motif of OsMAPK6. In near-isogenic lines (NILs), the log6-D allele increased grain length and grain yield of Guichao 2 (GC2), Teqing (TQ), and 93-11. Sequence analysis revealed 10 OsMAPK6 haplotypes, with xian (indica) and geng (japonica) harboring different haplotypes. Our findings shed light on the function of MAPKs and offer a novel dominant allele for improving the grain yield of rice.

Common wheat (Triticum aestivum) is a hexaploid plant (AABBDD) derived from genetically related tetraploid wheat T. turgidum (AABB) and a diploid goatgrass Aegilops tauschii (DD). Recent advances in sequencing technology and genome assembly strategies allow the acquisition of multiple wheat genomes, calling for a centralized database to store, manage and query the genomics information in a manner to reflect their evolutionary relationship and to perform effective comparative genome analysis. Here, we built WheatGene, a database that contains five wheat genomes of 318,102 genes and 945,900 transcripts and their expression information in 998 RNA-seq samples that can be searched and compared in an interactive manner. WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information. The database was accessible through a web browser with species, search, gene expression, tools, and literature entries. Tools available were BLAST, synteny viewer, map viewer, JBrowse, data downloads, gene expression heatmap and bar chart, and homologs viewer. Moreover, the map viewer connected genomics data with genetic maps and QTL that can be searched for markers for molecular breeding. WheatGene was developed with open-source modules and libraries. WheatGene is available at http://wheatgene.agrinome.org.