PidTools: Algorithm and web tools for crop pedigree identification analysis.

Crop pedigrees incorporate information on the kinship and genetic evolutionary history of breeding materials. Complete and accurate pedigree information is vital for effective genetic improvement of crops and maximal exploitation of heterosis in crop production. It is difficult for breeders to accurately extrapolate the selection of germplasm resources with missing genealogical information based on breeding experience.

Genomic analysis of a new heterotic maize group reveals key loci for pedigree breeding.

Genome-wide analyses of maize populations have clarified the genetic basis of crop domestication and improvement. However, limited information is available on how breeding improvement reshaped the genome in the process of the formation of heterotic groups. In this study, we identified a new heterotic group (X group) based on an examination of 512 Chinese maize inbred lines.

Development of Omni InDel and supporting database for maize.

Insertions-deletions (InDels) are the second most abundant molecular marker in the genome and have been widely used in molecular biology research along with simple sequence repeats (SSR) and single-nucleotide polymorphisms (SNP). However, InDel variant mining and marker development usually focuses on a single type of dimorphic InDel, which does not reflect the overall InDel diversity across the genome. Here, we developed Omni InDels for maize, soybean, and rice based on sequencing data and genome assembly that included InDel variants with base lengths from 1 bp to several Mb, and we conducted a detailed classification of Omni InDels.

Trash to treasure: lactate and protein lactylation in maize root impacts response to drought.

Lactate, protein lactylation (Kla), and specifically histone lactylation have recently been shown to regulate antipathogenic immune responses in mammals. Herein, after we confirmed the presence and accumulation of lactate in maize roots under drought conditions, a lactylome profiling analysis revealed that Kla modifications were invariably present in maize roots, that there were obvious differences in the lactylomes of drought-sensitive (B73) vs. drought-tolerant (Jing2416) lines, and that growing Jing2416 under drought conditions caused significant decreases in the lactylation of multiple enzymes responsible for fatty acid degradation.

Genetic basis of the oil biosynthesis in ultra-high-oil maize grains with an oil content exceeding 20.

Vegetable oil is an important part of the human diet and has multiple industrial uses. The rapid increase in vegetable oil consumption has necessitated the development of viable methods for optimizing the oil content of plants. The key genes regulating the biosynthesis of maize grain oil remain mostly uncharacterized.

A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340.

Background: Maize is an important model organism for genetics and genomics research. Though reference genomes of maize are available, some genomes of important genetic germplasms for maize breeding are still lacking, for instance, the cultivar Dan340, which is a backbone inbred line of the LvDa Red Cob Group with several desirable characteristics. In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by using long HiFi reads, short reads, and Hi-C.

De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis.

Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal production. However, the molecular mechanisms of heterosis remain obscure. Here we show that structural variants (SVs) between the parental lines have a predominant role underpinning maize heterosis.

Influential factors and transcriptome analyses of immature diploid embryo anthocyanin accumulation in maize.

Background: Anthocyanins are widely applied as a marker for haploid identification after haploid induction in maize. However, the factors affecting anthocyanin biosynthesis in immature embryos and the genes regulating this process remain unclear.

Results: In this study, we analyzed the influence of genetic background of the male and female parents, embryo age and light exposure on anthocyanin accumulation in embryos.

ORF355 confers enhanced salinity stress adaptability to S-type cytoplasmic male sterility maize by modulating the mitochondrial metabolic homeostasis.

Moderate stimuli in mitochondria improve wide-ranging stress adaptability in animals, but whether mitochondria play similar roles in plants is largely unknown. Here, we report the enhanced stress adaptability of S-type cytoplasmic male sterility (CMS-S) maize and its association with mild expression of sterilizing gene ORF355. A CMS-S maize line exhibited superior growth potential and higher yield than those of the near-isogenic N-type line in saline fields.

Comparative analysis of mitochondrial genomes of maize CMS-S subtypes provides new insights into male sterility stability.

Background: Cytoplasmic male sterility (CMS) is a trait of economic importance in the production of hybrid seeds. In CMS-S maize, exerted anthers appear frequently in florets of field-grown female populations where only complete male-sterile plants were expected. It has been reported that these reversions are associated with the loss of sterility-conferring regions or other rearrangements in the mitochondrial genome.

Chilling Tolerance in Maize: Insights into Advances-Toward Physio-Biochemical Responses' and QTL/Genes' Identification.

Maize, a major staple cereal crop in global food supply, is a thermophilic and short-day C4 plant sensitive to low-temperature stress. A low temperature is among the most severe agro-meteorological hazards in maize-growing areas. This review covers the latest research and progress in the field of chilling tolerance in maize in the last 40 years.

Characteristics and candidate genes associated with excellent stalk strength in maize ( L.).

Lodging is a major problem in maize production, which seriously affects yield and hinders mechanized harvesting. Improving stalk strength is an effective way to improve lodging. The maize inbred line Jing2416 (J2416) was an elite germplasm in maize breeding which had strong stalk mechanical strength.

Cloning southern corn rust resistant gene RppK and its cognate gene AvrRppK from Puccinia polysora.

Broad-spectrum resistance has great values for crop breeding. However, its mechanisms are largely unknown. Here, we report the cloning of a maize NLR gene, RppK, for resistance against southern corn rust (SCR) and its cognate Avr gene, AvrRppK, from Puccinia polysora (the causal pathogen of SCR).

, Encoding a Typical CC-NBS-LRR Protein, Confers Resistance to Southern Corn Rust in Maize.

Southern corn rust (SCR) caused by Underw. poses a major threat to maize production worldwide. The utilization of host SCR-resistance genes and the cultivation of resistant cultivars are the most effective, economical strategies for controlling SCR.

A newly characterized allele of ZmR1 increases anthocyanin content in whole maize plant and the regulation mechanism of different ZmR1 alleles.

The novel ZmR1 allele for maize anthocyanin synthesis was identified, and the biological function and regulatory molecular mechanisms of three ZmR1 alleles were unveiled. Anthocyanins in maize are valuable to human health. The R1 gene family is one of the important regulatory genes for the tissue-specific distribution of anthocyanins.

iTRAQ-based quantitative proteomic analysis provides insight into the drought-stress response in maize seedlings.

Drought is a major abiotic stress that harms plant cell physiology and limits the growth and productivity of crops. Maize (Zea mays L.), one of the most drought-susceptible crops, is a major food source for humans and an important resource for industrial bioenergy production; therefore, understanding the mechanisms of the drought response is essential for maize improvement.

HTPdb and HTPtools: Exploiting maize haplotype-tag polymorphisms for germplasm resource analyses and genomics-informed breeding.

Along with rapid advances in high-throughput-sequencing technology, the development and application of molecular markers has been critical for the progress that has been made in crop breeding and genetic research. Desirable molecular markers should be able to rapidly genotype tens of thousands of breeding accessions with tens to hundreds of markers. In this study, we developed a multiplex molecular marker, the haplotype-tag polymorphism (HTP), that integrates Maize6H-60K array data from 3,587 maize inbred lines with 6,375 blocks from the recombination block map.

Genome-wide identification and characterization of the MAPKKK, MKK, and MPK families in Chinese elite maize inbred line Huangzaosi.

Mitogen-activated protein kinase (MAPK or MPK) cascades consist of three protein kinase components, MAPK kinase kinases (MAPKKKs), MAPK kinases (MKKs and MPKs), which are indispensable for various plant physiological processes. The functions of MAPK families have been extensively studied in maize (Zea mays L.) and other plant species, but little is known about MAPK families in the elite Chinese maize line Huangzaosi (hzs).

Diversity of endophytic bacteria in hybrid maize seeds and Bacillus mojavensis J2416-7 may be capable of vertical transmission.

The diversity of endophytic bacteria in the progeny is related to the parental lines. In this study, the traditional separation method was used to study the dominant endophytic bacteria of the shared paternal line and its pollen, different maternal lines and their F1 progeny. And the results showed that the dominant endophytic bacteria in maize seeds and the pollen were Bacillus and Pantoea.

Target-oriented prioritization: targeted selection strategy by integrating organismal and molecular traits through predictive analytics in breeding.

Genomic prediction in crop breeding is hindered by modeling on limited phenotypic traits. We propose an integrative multi-trait breeding strategy via machine learning algorithm, target-oriented prioritization (TOP). Using a large hybrid maize population, we demonstrate that the accuracy for identifying a candidate that is phenotypically closest to an ideotype, or target variety, achieves up to 91%.

Comprehensive analysis of MAPK cascade genes in sorghum (Sorghum bicolor L.) reveals SbMPK14 as a potential target for drought sensitivity regulation.

The mitogen-activated protein kinase (MAPK) cascade plays a crucial role in regulating many important biological processes in plants. Here, we identified and characterized eight MAPKK and 49 MAPKKK genes in sorghum and analyzed their differential expression under drought treatment; we also characterized 16 sorghum MAPK genes. RNA-seq analysis revealed that 10 MAPK cascade genes were involved in drought stress response at the transcriptome level in sorghum.

A design optimized prime editor with expanded scope and capability in plants.

The ability to manipulate the genome in a programmable manner has illuminated biology and shown promise in plant breeding. Prime editing, a versatile gene-editing approach that directly writes new genetic information into a specified DNA site without requiring double-strand DNA breaks, suffers from low efficiency in plants. In this study, N-terminal reverse transcriptase-Cas9 nickase fusion performed better in rice than the commonly applied C-terminal fusion.

Natural variation of ZmCGT1 is responsible for isoorientin accumulation in maize silk.

Maize (Zea mays L.) silk contains high levels of flavonoids and is widely used to promote human health. Isoorientin, a natural C-glycoside flavone abundant in maize silk, has attracted considerable attention due to its potential value.