# positions[].organizations[].parent[].label
College of Agriculture and Life Sciences

# overview
My research is focused on Genetics, genomics, systems genomics, and gene-based breeding in crop plants, such as corn, cotton, wheat, and rice, particularly development of genomic and systems biological knowledge and new or advanced technologies for enhanced crop research and breeding. These include re-establishing of the molecular basis and mechanisms of genetics and biology: DNA "Jigsaw Puzzle" Structure Theory; accurate, sensitive, rapid, high-throughput, and cost-efficient cloning and characterization of genes controlling biological traits of agronomic importance using artificial intelligence-powered technology that we recently invented, AI-gExpress; deciphering of the molecular mechanisms of biological traits of importance such as quantitative genetics, epigenetics, crop yield, crop quality, heterosis, and plant polyploidization; and development of AI-powered molecular toolkits and associated pipelines for next-generation enhanced crop breeding, such as AI-powered gene-based breeding (AI-GBB) and crop production such as AI-powered gene-based precision agriculture (AI-GBPA). It has been demonstrated that AI-gExpress enables accurate (>99%), sensitive (can identify most, if not all, of the genes controlling biological traits in a species), rapid (1 - 2 scientist years), high-throughput (10,000 genes/scientist year), and cost-efficient (>$1,000/gene) identification of genes controlling agronomic traits in any species, including plants, animals, and humans, regardless of genome size, genome complexity, ploidy level, and availability of genomic resources and knowledge. It has been shown that AI-GBB can be performed throughput the entire breeding process in a manufactory manner, is dozens to hundreds-fold more powerful and more productive, 3 - 5 years faster, and dozens-fold more cost-efficient than the current breeding methods, including genomics-assisted breeding, and can further improve the current best varieties by 73% - 118%.

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
Bacterial Artificial Chromosome (bac) Library

# keywords[]
3002 Agriculture, Land And Farm Management

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# educationAndTraining[].organization.label
University of California, Davis - (Davis, California, United States)

# publications[].label
Characterization and distribution of an interspersed repeated nucleotide sequence from Lophopyrum elongatum and mapping of a segregation-distortion factor with it.

# publications[].label
A BAC- and BIBAC-based physical map of the soybean genome.

# publications[].label
A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L.

# publications[].label
A BAC-based physical map of the chicken genome.

# publications[].label
Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population

# publications[].label
Construction of tomato genomic DNA libraries in a binaryBAC (BIBAC) vector

# publications[].label
Cloning, characterization, and evolution of the NBS-LRR-encoding resistance gene analogue family in polyploid cotton (Gossypium hirsutum L.).

# publications[].label
A plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence.

# publications[].label
Phenotypic and molecular dissection of grain quality using the USDA rice mini-core collection.

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

# publications[].label
Construction and characterization of three BAC libraries for analysis of the chicken genome.

# publications[].label
Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Genome physical mapping of polyploids: a BIBAC physical map of cultivated tetraploid cotton, Gossypium hirsutum L.

# publications[].label
Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum.

# publications[].label
Construction of two BAC libraries from half-smooth tongue sole Cynoglossus semilaevis and identification of clones containing candidate sex-determination genes.

# publications[].label
Genetic mapping of jointless-2 to tomato chromosome 12 using RFLP and RAPD markers

# publications[].label
Penaeid shrimp genome provides insights into benthic adaptation and frequent molting.

# publications[].label
Construction and characterization of a bacterial artificial chromosome (BAC) library of Pacific white shrimp, Litopenaeus vannamei.

# publications[].label
An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence.

# publications[].label
Physical mapping of the rice genome with BACs.

# publications[].label
A detailed physical map of the horse Y chromosome.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Phylogenetic analysis of Gossypium L. using restriction fragment length polymorphism of repeated sequences.

# publications[].label
Construction and characterization of two bacterial artificial chromosome libraries of Zhikong scallop, Chlamys farreri Jones et Preston, and identification of BAC clones containing the genes involved in its innate immune system.

# publications[].id
A BAC library of Rosa chinensis cv. Old Blush

# publications[].label
Toward positional cloning of everblooming gene (evb) in plants

# publications[].label
WholeGenome Physical Mapping: An Overview on Methods for DNA Fingerprinting

# publications[].label
One large-insert plant-transformation-competent BIBAC library and three BAC libraries of Japonica rice for genome research in rice and other grasses.

# publications[].label
Organization and evolution of the 5S ribosomal RNA gene family in wheat and related species

# publications[].label
BLUEPRINT FOR THE CONSTRUCTION OF A FUNCTIONAL INTEGRATIVE MAP OF THE APPLE GENOME

# publications[].publisher
International Society for Horticultural Science (ISHS)

# publications[].label
Map-based cloning in crop plants. Tomato as a model system: I. Genetic and physical mapping of jointless.

# publications[].label
Fine genetic mapping and BAC contig development for the citrus tristeza virus resistance gene locus in Poncirus trifoliata (Raf.).

# publications[].label
Construction of a BAC library and generation of BAC end sequence-tagged connectors for genome sequencing of the African malaria mosquito Anopheles gambiae.

# publications[].label
Construction and characterization of a bacterial artificial chromosome library of thermo-sensitive genie male-sterile rice 5460S

# publications[].label
Wet laboratory tools widely used in plant genomics.

# publications[].label
Conserved synteny of genes between chromosome 15 of Bombyx mori and a chromosome of Manduca sexta shown by five-color BAC-FISH.

# publications[].label
Apple contains receptor-like genes homologous to the Cladosporium fulvum resistance gene family of tomato with a cluster of genes cosegregating with Vf apple scab resistance.

# publications[].label
Construction and characterisation of a large DNA insert library from the D genome of wheat

# publications[].label
Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research.

# publications[].label
Construction of two BAC libraries from cucumber (Cucumis sativus L.) and identification of clones linked to yield component quantitative trait loci.

# publications[].label
Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage, and contig map quality.

# publications[].label
Preparation of megabasesize DNA from plant nuclei

# publications[].label
Vernalization response of domesticated  wild chickpea progeny is subject to strong genotype by environment interaction

# publications[].label
Construction of a contig of BAC clones spanning the region of the apple scab avirulence gene AvrVg.

# publications[].label
Interactions among genomic structure, function, and evolution revealed by comprehensive analysis of the Arabidopsis thaliana genome.

# publications[].label
Construction of a quinoa (Chenopodium quinoa Willd.) BAC library and its use in identifying genes encoding seed storage proteins.

# publications[].label
Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis.

# publications[].label
Cloning and characterization of homeologous cellulose synthase catalytic subunit 2 genes from allotetraploid cotton (Gossypium hirsutum L.).

# publications[].label
A bacterial artificial chromosome-based physical map of Manihot esculenta ssp. flabellifolia

# publications[].label
Quantification of gene expression while taking into account RNA alternative splicing.

# publications[].label
Construction of a 550 kb BAC contig spanning the genomic region containing the apple scab resistance gene Vf.

# publications[].label
Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping.

# publications[].label
Application of molecular tools for study of the phylogeny of diploid and polyploid taxa in Triticeae

# publications[].label
Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L.

# publications[].label
An integrated BAC and genome sequence physical map of Phytophthora sojae.

# publications[].label
Construction of a bacterial artificial chromosome (BAC) library for citrus and identification of BAC contigs containing resistance gene candidates

# publications[].label
Genotypic variation among arcobacter isolates from a farrow-to-finish swine facility.

# publications[].label
Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors.

# publications[].label
Independent selection for seed free tryptophan content and vernalization response in chickpea domestication

# publications[].label
The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max.

# publications[].label
A plant-transformation-competent BIBAC library of ginseng (Panax ginseng C. A. Meyer) for functional genomics research and characterization of genes involved in ginsenoside biosynthesis

# publications[].label
Reconstruction of the phylogeny of the genus Triticum from variation in repeated nucleotide sequences.

# publications[].label
Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping.

# publications[].label
Construction and characterization of a BIBAC library of Jatropha curcas L. and identification of BIBAC clones containing genes associated with fatty acid metabolism

# publications[].label
Accurate prediction of maize grain yield using its contributing genes for gene-based breeding.

# publications[].label
Construction and characterization of a plant transformation-competent BIBAC library of the black Sigatoka-resistant banana Musa acuminata cv. Tuu Gia (AA).

# publications[].label
A plant-transformation-competent BIBAC library from the Arabidopsis thaliana Landsberg ecotype for functional and comparative genomics.

# publications[].label
Characterization of a plant-transformation-ready large-insert BIBAC library of Arabidopsis and bombardment transformation of a large-insert BIBAC of the library into tobacco.

# publications[].label
Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species.

# publications[].label
Two large-insert soybean genomic libraries constructed in a binary vector: applications in chromosome walking and genome wide physical mapping

# publications[].label
A binary vector-based large insert library for Brassica napus and identification of clones linked to a fertility restorer locus for Ogura cytoplasmic male sterility (CMS).

# publications[].label
A simple method for isolation of megabase DNA from cotton

# publications[].label
Genomic DNA Libraries and Physical Mapping

# publications[].label
Construction of BAC and BIBAC libraries from sunflower and identification of linkage group-specific clones by overgo hybridization.

# publications[].label
Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.).

# publications[].label
Construction of a binary BAC library for an apomictic monosomic addition line of Beta corolliflora in sugar beet and identification of the clones derived from the alien chromosome.

# publications[].label
A BAC-based physical map of Zhikong scallop (Chlamys farreri Jones et Preston).

# publications[].label
Cassava genome from a wild ancestor to cultivated varieties.

# publications[].label
Structural diversity and differential transcription of the patatin multicopy gene family during potato tuber development.

# publications[].label
Genetic Relationship in Cicer Sp. Expose Evidence for Geneflow between the Cultigen and Its Wild Progenitor.

# publications[].label
Diploid ancestry and evolution of Triticum kotschyi and T. peregrinum examined using variation in repeated nucleotide sequences

# publications[].id
a robust physical map of Penicillium chrysogenum -: art. no. e50

# publications[].label
Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis

# publications[].label
Isolation of megabase-size DNA from sorghum and applications for physical mapping and bacterial and yeast artificial chromosome library construction

# publications[].label
An improved method of plant megabase DNA isolation in agarose microbeads suitable for physical mapping and YAC cloning.

# publications[].label
Transcriptome Analysis of Green Peach Aphid (Myzus persicae): Insight into Developmental Regulation and Inter-Species Divergence.

# publications[].label
The genome origin and evolution of hexaploid Triticum crassum and Triticum syriacum determined from variation in repeated nucleotide sequences

# publications[].label
A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes.

# publications[].label
Map-based cloning in crop plants: tomato as a model system II. Isolation and characterization of a set of overlapping yeast artificial chromosomes encompassing the jointless locus.

# publications[].label
BAC library development for allotetraploid Leymus (Triticeae) wildryes enable comparative genetic analysis of lax-barrenstalk1 orthogene sequences and growth habit QTLs

# publications[].label
Mapping quantitative trait loci in chickpea associated with time to flowering and resistance to Didymella rabiei the causal agent of Ascochyta blight.

# publications[].label
Biometric Analyses of the Inheritance of Resistance to Didymella rabiei in Chickpea.

# publications[].label
Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Distribution and sequence analysis of the centromere-associated repetitive element CEN38 of Sorghum bicolor (Poaceae).

# publications[].label
A bacterial artificial chromosome based physical map of the Ustilago maydis genome.

# publications[].label
Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research.

# publications[].label
Extensive conserved synteny of genes between the karyotypes of Manduca sexta and Bombyx mori revealed by BAC-FISH mapping.

# publications[].label
Genetic and physical mapping of a rice blast resistance locus, Pi-CO39(t), that corresponds to the avirulence gene AVR1-CO39 of Magnaporthe grisea.

# publications[].label
Construction and characterization of a bacterial artificial chromosome library of apple

# publications[].label
Construction of bacterial artificial chromosome libraries for Zhikong Scallop Chlamys farreri

# publications[].label
Quantitative Trait Loci for Cold Tolerance in Chickpea

# publications[].label
Identification and characterisation of a melon genomic region containing a resistance gene cluster from a constructed BAC library. Microcolinearity between Cucumis melo and Arabidopsis thaliana.

# publications[].label
Construction of two BAC libraries from the wild Mexican diploid potato, Solanum pinnatisectum, and the identification of clones near the late blight and Colorado potato beetle resistance loci.

# publications[].label
Isolation of repeated DNA sequences from Lophopyrum elongatum for detection of Lophopyrum chromatin in wheat genomes

# publications[].label
A bac library constructed to the rice cultivar "Minghui 63" for cloning genes of agronomic importance

# publications[].label
Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].label
Identification and characterization of a repertoire of genes differentially expressed in developing top ear shoots between a superior hybrid and its parental inbreds in Zea mays L.

# researcherOn[].label
Development of Gene-Based Breeding (GBB) for Crops of Agricultural Importance

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Large-scale Cloning of Genes Controlling Agronomic Traits and Deciphering of the Molecular Bases Underlying Yield and Quality to Develop a Gene-based Breeding System in Important Crops

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# streetAddress
Texas A&M University and Texas A&M AgriLife Research; Department of Soil & Crop Sciences; 2474 TAMUS

# organizations[]
College of Agriculture and Life Sciences

# schools[]
College of Agriculture and Life Sciences

# inTheNews[].label
National honors bestowed on Texas A&M faculty

# etdChairOf[].label
Liu, Yun-Hua (2008-12). The dna. Master's Thesis.

# etdChairOf[].label
Zhi, Hui (2010-12). Molecular Basis of Heterosis in Maize: Genetic Correlation and 3-Dimensional Network Between Gene Expression and Grain Yield Trait Heterosis. Master's Thesis.

# etdChairOf[].label
Liu, Yun Hua (2014-08). Molecular Basis of Quantitative Genetics Revealed by Cloning and Analysis of 474 Genes Controlling Fiber Length in Cotton. Doctoral Dissertation.