Construction of a single nucleotide polymorphism linkage map and identification of quantitative trait loci controlling heat tolerance in cowpea, Vigna unguiculata (L.) Walp.

Plant tolerance to heat or high temperature is crucial to crop production, especially in the situation of elevated temperature resulting from global climate change. Cowpea, Vigna unguiculata (L.) Walp., is an internationally important legume food crop and an excellent pool of genes for numerous traits resilient to environmental extremes, particularly heat and drought. Here, we report a single nucleotide polymorphism (SNP) genetic map for cowpea and identification of the loci controlling the heat tolerance in the species. The SNP map consists of 531 bins containing 4,154 SNPs grouped into 11 linkage groups, and collectively spans 1,084.7 cM, thus having a density of one SNP in 0.26 cM or 149 kb. The 11 linkage groups of the map were aligned to the 11 cowpea chromosomes. Quantitative trait locus (QTL) mapping identified nine QTLs responsible for the cowpea heat tolerance on seven of the 11 chromosomes, with each QTL explaining 6.5-21.8% of heat tolerance phenotypic variation. Moreover, we aligned these nine QTLs to the cowpea genome. Each of the QTLs was positioned in a genomic region ranging from 209,000 bp to 12,590,450 bp, and the QTL with the largest effect (21.8%) on heat tolerance, qHT4-1, was located within an interval of only 234,195 bp. These results provide SNP markers useful for marker-assisted selection for heat tolerance and lay a foundation for cloning, characterization, and applications of the genes controlling the cowpea heat tolerance for heat tolerance genetic improvement in cowpea and related crops.

[Study on metabolites in vivo of Dangefentong Capsules based on UHPLC-Q/Orbitrap-MS/MS].

Dangefentong Capsules is a new traditional Chinese medicine preparation for the treatment of diabetic peripheral neuropathy. It is based on the Salviae Miltiorrhizae Radix et Rhizoma-Puerariae Lobatae Radix herb pair with salvianolic acids, tanshinones and pueraria flavonoids as main components. Studying the chemical composition in vivo of Dangefentong Capsules and its metabolites is of great significance for making clear its pharmacodynamic material basis and the action mechanism. The UHPLC-Q/Orbitrap-MS/MS was applied to rapidly analyze the metabolites and metabolic pathways of Dangefentong Capsules in Beagle dogs after gavage. Eclipse plus C_(18) column(2.1 mm×50 mm, 1.8 µm) was used, and gradient elution was performed with 0.1% formic acid aqueous solution(A)-formic acid acetonitrile solution(B). A heated electrospray ion source(HESI) was employed. The scanning mode was set as the positive and negative ion mode, and the mass scanning range was m/z 100-1 000. The plasma, urine and feces samples were collected after male Beagle dogs were administered with Dangefentong Capsules. The prototype components and metabolites were identified by UHPLC-Q/Orbitrap-MS/MS analysis combined with reference substances and references. The results showed that 107 chemical components were identified, including 58 prototype components and 49 metabolites. The identified prototype components included 42 components from Salviae Miltiorrhizae Radix et Rhizoma and 16 components from Puerariae Lobatae Radix. The metabolites consist of 21 and 28 metabolites of Salviae Miltiorrhizae Radix et Rhizoma and Puerariae Lobatae Radix, respectively. They are mainly derived from the methylation, hydroxylation, sulfation and glucuronidation of salvianolic acids, tanshinones and pueraria flavonoids. This research rapi-dly analyzes the chemical components in vivo of Beagle dogs administered with Dangefentong Capsules, laying a basis for illustrating the pharmacodynamic material basis and mechanism of Dangefentong Capsules.

Single-cell RNA-seq reveals mRNAs and lncRNAs important for oocytes in vitro matured in pigs.

The faithful execution of molecular programme underlying oocyte maturation and meiosis is vital to generate competent haploid gametes for efficient mammalian reproduction. However, the organization and principle of molecular circuits and modules for oocyte meiosis remain obscure. Here, we employed the recently developed single-cell RNA-seq technique to profile the transcriptomes of germinal vesicle (GV) and metaphase II (MII) oocytes, aiming to discover the dynamic changes of mRNAs and long non-coding RNAs (lncRNAs) during oocyte in vitro meiotic maturation. During the transition from GV to MII, total number of detected RNAs (mRNAs and lncRNAs) in oocytes decreased. Moreover, 1,807 (602 up- and 1,205 down-regulated) mRNAs and 313 (177 up- and 136 down-regulated) lncRNAs were significantly differentially expressed (DE), i.e., more mRNAs down-regulated, but more lncRNAs up-regulated. During maturation of pig oocytes, mitochondrial mRNAs were actively transcribed, eight of which (ND6, ND5, CYTB, ND1, ND2, COX1, COX2 and COX3) were significantly up-regulated. Both DE mRNAs and targets of DE lncRNAs were enriched in multiple biological and signal pathways potentially associated with oocyte meiosis. Highly abundantly expressed mRNAs (including DNMT1, UHRF2, PCNA, ARMC1, BTG4, ASNS and SEP11) and lncRNAs were also discovered. Weighted gene co-expression network analysis (WGCNA) revealed 20 hub mRNAs in three modules to be important for oocyte meiosis and maturation. Taken together, our findings provide insights and resources for further functional investigation of mRNAs/lncRNAs in in vitro meiotic maturation of pig oocytes.

Accurate prediction of maize grain yield using its contributing genes for gene-based breeding.

Accurately predicting the phenotypes of complex traits is crucial to enhanced breeding in plants and livestock, and to enhanced medicine in humans. Here we reports the first study accurately predicting complex traits using their contributing genes, especially their number of favorable alleles (NFAs), genotypes and transcript expressions, with the grain yield of maize, Zea mays L. When the NFAs or genotypes of only 27 SNP/InDel-containing grain yield genes were used, a prediction accuracy of r = 0.52 or 0.49 was obtained. When the expressions of grain yield gene transcripts were used, a plateaued prediction accuracy of r = 0.84 was achieved. When the phenotypes predicted with two or three of the genic datasets were used for progeny selection, the selected lines were completely consistent with those selected by phenotypic selection. Therefore, the genes controlling complex traits enable accurately predicting their phenotypes, thus desirable for gene-based breeding in crop plants.

[Content determination of phenolic acids in fresh Salvia miltiorrhiza and effect of polyphenol oxidase on content].

There is no consensus on the content, accumulation, transformation and content determination methods of phenolic acids in fresh Salvia miltiorrhiza. In order to find out the true content of phenolic acids in fresh S. miltiorrhiza, a variety of treatment me-thods were used in this study to prepare sample solution. The content changes of phenolic acids in S. miltiorrhiza samples with different dehydration rates were investigated during drying and shade drying processes. Polyphenol oxidase(PPO) of S. miltiorrhiza was extracted and purified by ammonium sulfate precipitation and dialysis to investigate the enzymatic properties. The content of rosmarinic acid, lithosperic acid and S. nolic acid B in S. miltiorrhiza was determined by UPLC. The results showed that the content of phenolic acids in fresh S. miltiorrhiza was highest when it was homogenized with 1 mol·L~(-1) HCl solution or 1 mol·L~(-1) HCl methanol solution. There was no significant difference in the content of phenolic acids in S. miltiorrhiza with different dehydration rates, indicating that there was no correlation between phenolic acid content and dehydration rate. The optimum pH of S. miltiorrhiza PPO was 7.6 and the optimum temperature was 40 ℃. With catechol as substrate, S. miltiorrhiza PPO had the enzymatic browning reaction which was in compliance with Michaelis equation, with Michaelis constant K_m of 0.12 mol·L~(-1) and V_(max) of 588.23 U·min~(-1). The inhibitory effect of citric acid, disodium ethylenediamine tetraacetate, ascorbic acid and sodium sulfite on S. miltiorrhiza PPO increased with the increase of inhibitor concentration, and sodium sulfite showed the strongest inhibitory effect. The present study proved that there were a large number of phenolic acids in fresh S. miltiorrhiza, which were the secondary metabolite of primitive accumulation during the growth of S. miltiorrhiza, rather than the induced product of postharvest drying and dehydration stress. This study has reference value and significance for the cultivation, harvest and processing of S. miltiorrhiza.

[Pharmacokinetics of eight active ingredients of Salviae Miltiorrhizae Radix et Rhizoma-Puerariae Lobatae Radix combination in rats].

To reveal the rationality of compatibility of Salviae Miltiorrhizae Radix et Rhizoma(SMRR) and Puerariae Lobatae Radix(PLR) from the perspective of pharmacokinetics, this study established a UPLC-MS/MS method for quantitative determination of PLR flavonoids(3'-hydroxy puerarin, puerarin, puerarin 6″-O-xyloside, 3'-methoxy puerarin, puerarin apioside) and salvianolic acids and tanshinones(salvianolic acid B, cryptotanshinone, and tanshinone Ⅱ_A) in plasma of rats. Rats were given SMRR extract, PLR extract, and SMRR-PLR extract by gavage and then plasma was collected at different time. UPLC separation was performed under the following conditions: Eclipse C_(18) column(2.1 mm×50 mm, 1.8 µm), 0.1% formic acid in water(A)-0.1% formic acid in acetonitrile(B) as mobile phase for gradient elution. Conditions for MS are as below: multiple reaction monitoring(MRM), ESI~(+/-). Comprehensive validation of the UPLC-MS/MS method(specifically, from the aspects of calibration curve, precision, accuracy, repeatability, stability, matrix effect, extract recovery) was performed and the result demonstrated that it complied with quantitative analysis requirements for biological samples. Compared with SMRR extract alone or PLR extract alone, SMRR-PLR extract significantly increased the AUC and C_(max) of PLR flavonoids and tanshinones in rat plasma, suggesting that the combination of SMRR and PLR promoted the absorption of the above components. The underlying mechanism needs to be further studied.

Quantitative trait loci influencing days to flowering and plant height in cowpea, Vigna unguiculata (L.) Walp.

Cowpea (Vigna unguiculate (L.) Walp.) is a worldwide important multifunctional legume crop for food grain, vegetable, fodder, and cover crop. Nevertheless, only limited research has been conducted on agronomic traits. Here, we report quantitative trait locus (QTL) analysis of the days to flowering (DTF) and plant height (PH) using a dense SNP linkage map recently developed from a recombinant inbred line (RIL) population derived from a cross between Golden Eye Cream and IT98K-476-8. The population was phenotyped for DTF and PH through field and greenhouse trials under two environments. The QTLs controlling these traits were mapped using multiple-environment combined and individual trial phenotypic data. The combined data analysis identified one major QTL (qDTF9.1) for DTF, and one major QTL (qPH9.1) and a minor QTL (qPH4.1) for PH. qDTF9.1 and qPH9.1 were adjacent to each other on Chromosome 9 and each explained 29.3% and 29.5% of the phenotypic variation (PVE), respectively. The individual trial data analysis identified a minor QTL (qDTF2.1) on Chromosome 2 for DTF and two minor QTLs (qPH4.1 and qPH4.2) on Chromosome 4 for PH, while the major QTLs, qDTF9.1 and qPH9.1, were consistently identified in all trials conducted. Epistasis analysis revealed that qDTF9.1 interacted with one locus on Chromosome 4, contributed 50% of the PVE, and qPH9.1 interacted with one locus on each of Chromosomes 4 and 6, contributing 30% and 23% of the PVE, respectively, suggesting that epistasis plays an important role in the trait performance. These results, therefore, provide a deeper understanding of the genetic architecture of plant DTF and PH, and molecular tools necessary for cloning the genes and for enhanced cowpea breeding.

Quantification of gene expression while taking into account RNA alternative splicing.

Gene expression has been widely used in functional genomics research; however, the gene expressions quantified with different methods have been frequently inconsistent, thus challenging the conclusions from such research. Here we have addressed this issue, while taking into account RNA alternative splicing. We found that when a gene was subjected to RNA alternative splicing, it was impossible or difficult to properly quantify the expression of a transcript of the gene or its overall expression using quantitative real-time PCR (qPCR), Northern hybridization, microarray, or serial analysis of gene expression. Shot-gun RNA-seq was the most proper to quantify the expression of a transcript or a gene in such cases. Moreover, the expressions of individual transcripts quantified by shot-gun RNA-seq were highly reproducible (r = 0.90-0.98) between individuals. Therefore, shot-gun or full-length RNA-seq should be the method of choice to properly quantify the expression of a transcript or a gene.

[Comparative study on free and bound phenolic acids before and after drying of Salvia miltiorrhiza].

There were significant differences in phenolic acid content between fresh and dried Salvia miltiorrhiza before and after drying. That is to say, the content of phenolic acid in S. miltiorrhiza significantly increased with the increase of dehydration during the drying process.In order to investigate the differences and transformation of free and bound phenolic acids before and after the drying process of S.miltiorrhiza, we studied hydrolysis method, hydrolysates and hydrolysis regularity of phenolic acids in S.miltiorrhiza. UPLC method was used to determine four main hydrolysates of bound phenolic acids, namely danshensu, caffeic acid dimer(SMND-309), caffeic acid, przewalskinic acid A(prolithosperic acid), and three main free phenolic acids in S.miltiorrhiza, namely rosmarinic acid, lithospermic acid, salvianolic acid B. The results of the acid-base hydrolysis experiment of salvianolic acid showed that the alkaline hydrolysis effect was significantly better than acid hydrolysis. The optimal alkaline hydrolysis condition was hydrolysis at 70 ℃ for 4 h with 2 mol·L~(-1) NaOH solution containing 1% ascorbic acid(Vit C). The hydrolysates of free phenolic acids were the same with the hydrolysates of bound phenolic acids. Fresh S.miltiorrhiza contains a low level of free phenolic acids and a high level of bound phenolic acids, which were exactly opposite to dried S.miltiorrhiza. It was suggested that a large amount of bound phenolic acids was accumulated during the growth of S.miltiorrhiza. These bound phenolic acids were coupled with polysaccharides on the cytoderm through ester bonds to form insoluble phenolic acids, which was not easy to be detected by conventional methods. However, during drying and dehydration processes, the bound phenolic acids were converted to a large amount of free phenolic acids under the action of the relevant enzyme.

Single-cell transcriptome sequencing reveals that cell division cycle 5-like protein is essential for porcine oocyte maturation.

The brilliant cresyl blue (BCB) test is used in both basic biological research and assisted reproduction to identify oocytes likely to be developmentally competent. However, the underlying molecular mechanism targeted by the BCB test is still unclear. To explore this question, we first confirmed that BCB-positive porcine oocytes had higher rates of meiotic maturation, better rates of cleavage and development into blastocysts, and lower death rates. Subsequent single-cell transcriptome sequencing on porcine germinal vesicle (GV)-stage oocytes identified 155 genes that were significantly differentially expressed between BCB-negative and BCB-positive oocytes. These included genes such as cdc5l, ldha, spata22, rgs2, paip1, wee1b, and hsp27, which are enriched in functionally important signaling pathways including cell cycle regulation, oocyte meiosis, spliceosome formation, and nucleotide excision repair. In BCB-positive GV oocytes that additionally had a lower frequency of DNA double-strand breaks, the CDC5L protein was significantly more abundant. cdc5l/CDC5L inhibition by short interference (si)RNA or antibody microinjection significantly impaired porcine oocyte meiotic maturation and subsequent parthenote development. Taken together, our single-oocyte sequencing data point to a potential new role for CDC5L in porcine oocyte meiosis and early embryo development, and supports further analysis of this protein in the context of the BCB test.

[Study on dynamic changes of chemical constituents during different drying processes of Salvia miltiorrhiza].

There is no consensus on the drying methods of Salvia miltiorrhiza in ancient and modern times,especially on the content of phenolic acid in fresh S. miltiorrhiza. In order to further explore the content of main components in fresh S. miltiorrhiza and study the dynamic changes during the drying process,the content of main components was used as the index in this study to evaluate the processing method,drying method,correlation between dehydration rate and component content for fresh S. miltiorrhiza. In addition,the sealed and unsealed parallel control groups were set to carry out verification test during the drying process. UPLC method was used for determination of seven main components including rosmarinic acid,lithosperic acid,salvianolic acid B,cryptotanshinone,tanshinoneⅠ,methylene salianolate and tanshinone ⅡAin S. miltiorrhiza. The results showed that the fresh S. miltiorrhiza contained low levels of phenolic acid,and the content of phenolic acid increased significantly with the increase of dehydration rate during drying process,while the change of tanshinone was not obvious. In the comparison of three drying methods,we found that drying at 50 ℃ was better than drying in the sun,and drying in the sun was superior to drying in the shade. So,drying at 50 ℃ was the best drying method. The correlation between dehydration and phenolic acid content of S. miltiorrhiza was analyzed by verification test and SPSS software,which further proved that the dehydration rate was significantly positively correlated with the content of phenolic acid components. This study provides reference for the production processing and drying methods of S. miltiorrhiza medicinal materials,which is of great significance for improving the quality of S. miltiorrhiza.

Drought stress modulates diurnal oscillations of circadian clock and drought-responsive genes in Oryza sativa L.

Endogenous circadian rhythms play a key role in regulating plant growth and development, and in allowing plants to respond and adapt to changing environments. To understand how drought regulates upland rice(Oryza sativa L.) IRAT109, we examined the expression levels of circadian clock and drought-responsive genes through real-time PCR. The results revealed that, first, drought reduced the relative expression level and amplitude of peak expression of several morning circadian clock components (such as OsPRRs, OsLHY and OsZTL1), increased the relative expression level and amplitude of some evening circadian clock components (such as OsTOC1, OsGI and OsELF3), but did not influence OsFKF1. Secondly, the relative expression level of most drought-responsive genes was generally increased, except for OsDST, a negative regulator. Lastly, expression rhythms of most drought-responsive genes were disturbed, but not that of OsCIPK12, OsCDPK7 and OsDREB1A. The results indicate that drought stress modulates the expression of circadian clock components and the interplay regulates diurnal oscillations of relative genes.

[Comparative Study on Volatile Oil Composition of Chuanxiong Rhizoma, Angelicae Sinensis Radix and Ligustici Rhizoma et Radix].

OBJECTIVE: To identify Chuanxiong Rhizoma,Angelicae Sinensis Radix and Ligustici Rhizoma et Radix by establishing the HPLC specific chromatograms of their volatile oil and to compare their specific peaks. METHODS: The HPLC method used methanol-water as mobile phase. Their specific peaks were analysed by HPLC-MS. RESULTS: Under the selected spectrum condition, their HPLC specific chromatograms were established. Senkyunolide A, butylphalide, coniferylferulate, E-ligustilide, Z-ligustilide, neocnidilide and E-butylidenephthalide were identified as specific peaks in chromatograms based on their MS data. CONCLUSION: This method is simple, accurate and available to identify Chuanxiong Rhizoma, Angelicae Sinensis Radix and Ligustici Rhizoma et Radix. It provides reference for quality control of their medicinal materials and Chinese Patent Medicine.

DNA is structured as a linear "jigsaw puzzle" in the genomes of Arabidopsis, rice, and budding yeast.

Knowledge of how a genome is structured and organized from its constituent elements is crucial to understanding its biology and evolution. Here, we report the genome structuring and organization pattern as revealed by systems analysis of the sequences of three model species, Arabidopsis, rice and yeast, at the whole-genome and chromosome levels. We found that all fundamental function elements (FFE) constituting the genomes, including genes (GEN), DNA transposable elements (DTE), retrotransposable elements (RTE), simple sequence repeats (SSR), and (or) low complexity repeats (LCR), are structured in a nonrandom and correlative manner, thus leading to a hypothesis that the DNA of the species is structured as a linear "jigsaw puzzle". Furthermore, we showed that different FFE differ in their importance in the formation and evolution of the DNA jigsaw puzzle structure between species. DTE and RTE play more important roles than GEN, LCR, and SSR in Arabidopsis, whereas GEN and RTE play more important roles than LCR, SSR, and DTE in rice. The genes having multiple recognized functions play more important roles than those having single functions. These results provide useful knowledge necessary for better understanding genome biology and evolution of the species and for effective molecular breeding of rice.

Receptor-interacting Protein Kinase 2 Is an Immunotherapy Target in Pancreatic Cancer.

Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal malignancy because of its aggressive nature and the paucity of effective treatment options. Almost all registered drugs have proven ineffective in addressing the needs of patients with PDAC. This is the result of a poor understanding of the unique tumor-immune microenvironment (TME) in PDAC. To identify druggable regulators of immunosuppressive TME, we performed a kinome- and membranome-focused CRISPR screening using orthotopic PDAC models. Our data showed that receptor-interacting protein kinase 2 (RIPK2) is a crucial driver of immune evasion of cytotoxic T-cell killing and that genetic or pharmacologic targeting of RIPK2 sensitizes PDAC to anti-programmed cell death protein 1 (anti-PD-1) immunotherapy, leading to prolonged survival or complete regression. Mechanistic studies revealed that tumor-intrinsic RIPK2 ablation disrupts desmoplastic TME and restores MHC class I (MHC-I) surface levels through eliminating NBR1-mediated autophagy-lysosomal degradation. Our results provide a rationale for a novel combination therapy consisting of RIPK2 inhibition and anti-PD-1 immunotherapy for PDAC. SIGNIFICANCE: PDAC is resistant to almost all available therapies, including immune checkpoint blockade. Through in vivo CRISPR screen, we identified that RIPK2 plays a crucial role in facilitating immune evasion by impeding antigen presentation and cytotoxic T-cell killing. Targeting tumor-intrinsic RIPK2 either genetically or pharmacologically improves PDAC to anti-PD-1 immunotherapy. See related commentary by Liu et al., p. 208 . This article is featured in Selected Articles from This Issue, p. 201.

Development of a model based on the age-adjusted Charlson comorbidity index to predict survival for resected perihilar cholangiocarcinoma.

BACKGROUND: Perihilar cholangiocarcinoma (pCCA) has a poor prognosis and urgently needs a better predictive method. The predictive value of the age-adjusted Charlson comorbidity index (ACCI) for the long-term prognosis of patients with multiple malignancies was recently reported. However, pCCA is one of the most surgically difficult gastrointestinal tumors with the poorest prognosis, and the value of the ACCI for the prognosis of pCCA patients after curative resection is unclear. AIM: To evaluate the prognostic value of the ACCI and to design an online clinical model for pCCA patients. METHODS: Consecutive pCCA patients after curative resection between 2010 and 2019 were enrolled from a multicenter database. The patients were randomly assigned 3:1 to training and validation cohorts. In the training and validation cohorts, all patients were divided into low-, moderate-, and high-ACCI groups. Kaplan-Meier curves were used to determine the impact of the ACCI on overall survival (OS) for pCCA patients, and multivariate Cox regression analysis was used to determine the independent risk factors affecting OS. An online clinical model based on the ACCI was developed and validated. The concordance index (C-index), calibration curve, and receiver operating characteristic (ROC) curve were used to evaluate the predictive performance and fit of this model. RESULTS: A total of 325 patients were included. There were 244 patients in the training cohort and 81 patients in the validation cohort. In the training cohort, 116, 91 and 37 patients were classified into the low-, moderate- and high-ACCI groups. The Kaplan-Meier curves showed that patients in the moderate- and high-ACCI groups had worse survival rates than those in the low-ACCI group. Multivariable analysis revealed that moderate and high ACCI scores were independently associated with OS in pCCA patients after curative resection. In addition, an online clinical model was developed that had ideal C-indexes of 0.725 and 0.675 for predicting OS in the training and validation cohorts. The calibration curve and ROC curve indicated that the model had a good fit and prediction performance. CONCLUSION: A high ACCI score may predict poor long-term survival in pCCA patients after curative resection. High-risk patients screened by the ACCI-based model should be given more clinical attention in terms of the management of comorbidities and postoperative follow-up.

Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors.

Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)-encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their 'surplus' genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms' phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism's morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.

Analysis of the genes controlling cotton fiber length reveals the molecular basis of plant breeding and the genetic potential of current cultivars for continued improvement.

Stagnated crop improvement has raised questions of whether and how current crop cultivars can be further improved. Genes are the core determinants of performance of all cultivars. Here, we report the molecular basis of plant breeding and address these questions by analyzing 226 GFL genes controlling and accurately predicting fiber length, an important breeding objective trait, in cotton (Gossypium sp.). We first identified the favorable allele and the number of favorable alleles (NFAs) of each GFL gene, calculated the total NFAs of the 226 GFL genes accumulated in 198 advanced breeding lines, and analyzed them against fiber lengths. Fiber lengths of the breeding lines were strongly correlated with the total NFAs of the GFL genes (r = 0.85, P < 0.0001), suggesting that accumulation of the favorable alleles of the genes controlling objective traits is the molecular basis of cotton breeding. Surprisingly, a breeding line with a fiber length of present cultivars having the longest fibers contained only about 51% of the total NFAs of the 226 GFL genes. The genetic potentials of current cultivars were then predicted using linear and non-linear models, respectively, revealing that a breeding line or cultivar with a fiber length of 33.8 mm could be further improved in fiber length by up to 118%. Finally, we showed that the genetic potential of such a breeding line can be realized through gene-based breeding. Therefore, these findings shed light on continued crop improvement in general and provide 740 genic biomarkers desirable for enhanced cotton fiber breeding.

Accurate prediction of complex traits for individuals and offspring from parents using a simple, rapid, and efficient method for gene-based breeding in cotton and maize.

Accurate, simple, rapid, and inexpensive prediction of complex traits controlled by numerous genes is paramount to enhanced plant breeding, animal breeding, and human medicine. Here we report a novel method that enables accurate, simple, and rapid prediction of complex traits of individuals or offspring from parents based on the number of favorable alleles (NFAs) of the genes controlling the objective traits. The NFAs of 226 cotton fiber length (GFL) genes and nine maize hybrid grain yield related (ZmF1GY) genes were directly used to predict cotton fiber lengths of individual plants and maize grain yields of F1 hybrids from parents, respectively, using prediction model-based methods as controls. The NFAs of the 226 GFL genes predicted cotton fiber lengths at an accuracy of 0.85, as the model methods and outperforming genomic prediction by 82 % - 170 %. The NFAs of the nine ZmF1GY genes predicted grain yields of maize hybrids from parents at an accuracy of 0.80, outperforming genomic prediction by 67 %. Moreover, the prediction accuracies of these traits were consistent across years, environments, and eco-agricultural systems. Importantly, the accurate prediction of these traits directly using the NFAs of the genes allows breeding to be performed in greenhouse, phytotron, or off-season, without the need of the model training and validation steps essential and costly for model-based genomic or genic prediction. Therefore, this new method dramatically outperforms the current model-based genomic methods used for phenotype prediction and streamlines the process of breeding, thus promising to substantially enhance current plant and animal breeding.

Genome-wide identification of genes enabling accurate prediction of hybrid performance from parents across environments and populations for gene-based breeding in maize.

Accurate prediction of hybrid offspring complex trait phenotype from parents is paramount to enhanced plant breeding, animal breeding, and human medicine. Here we report genome-wide identification of genes enabling accurate prediction of hybrid offspring complex traits from parents using maize grain yield as the target trait. We identified 181 ZmF1GY genes enabling prediction of maize (Zea mays L.) F1 hybrid grain yield from parents and tested their utility and efficiency for predicting F1 hybrid grain yields from parents using their expressions, genic SNPs, and number of favorable alleles (NFAs), respectively. The ZmF1GY genes predicted hybrid grain yields from parents at an accuracy of 0.86, presented by correlation coefficient between predicted and observed phenotypes, within an environment, 0.74 across environments, and 0.64 across populations, outperforming genomic prediction by 27-406%, 23%, and 40%, respectively. Furthermore, we identified nine of the ZmF1GY genes containing SNPs or InDels in parents that increased or decreased hybrid grain yields by 14-46%. When the NFAs of these nine ZmF1GY genes were used for hybrid grain yield prediction from parents, they predicted hybrid grain yields at an accuracy of 0.79, outperforming genomic prediction by 21% that was based on up to tens of thousands of genome-wide SNPs. These results demonstrate the feasibility of developing a gene toolkit for a species enabling gene-based breeding across environments and populations that is much more powerful and efficient than current breeding, thereby helping secure the world's food production. The methodology is applicable to all crops, livestock, and humans.