Qiuju Xia

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

About 8,000 years ago in the Fertile Crescent, a spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n = 14; DD) with the cultivated tetraploid wheat Triticum turgidum (2n = 4x = 28; AABB) resulted in hexaploid wheat (T. aestivum; 2n = 6x = 42; AABBDD). Wheat has since become a primary staple crop worldwide as a result of its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker’s flour. Here we describe sequencing the Ae. tauschii genome and obtaining a roughly 90-fold depth of short reads from libraries with various insert sizes, to gain a better understanding of this genetically complex plant. The assembled scaffolds represented 83.4% of the genome, of which 65.9% comprised transposable elements. We generated comprehensive RNA-Seq data and used it to identify 43,150 protein-coding genes, of which 30,697 (71.1%) were uniquely anchored to chromosomes with an integrated high-density genetic map. Whole-genome analysis revealed gene family expansion in Ae. tauschii of agronomically relevant gene families that were associated with disease resistance, abiotic stress tolerance and grain quality. This draft genome sequence provides insight into the environmental adaptation of bread wheat and can aid in defining the large and complicated genomes of wheat species.

Genome sequence of foxtail millet ( Setaria italica ) provides insights into grass evolution and biofuel potential

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C4 biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C4 photosynthesis pathway were also identified.

Development of Novel EST–SSRs from Sacred Lotus (Nelumbo nucifera Gaertn) and Their Utilization for the Genetic Diversity Analysis of N. nucifera

Expressed sequence tags (ESTs) provide a valuable resource for the development of simple sequence repeat (SSR) or microsatellite markers. This study identified SSRs within ESTs from Nelumbo nucifera (lotus or sacred lotus), developed markers from them, and assessed the potential of those markers for diversity analysis. Within 2207 ESTs from N. nucifera downloaded from GenBank, 1483 unigenes (303 contigs and 1180 singletons) were identified. After eliminating for redundancy, 125 SSR-containing ESTs were derived, and 71 unique SSRs were detected with an average density of one SSR per 13.04 kb. Dinucleotide repeats were the dominant motif in N. nucifera, whereas the sequences AG/TC/GA/CT, AAG/TTC/GAT/AGA, and AAAGCC were the most frequent of di-, tri-, and hexanucleotide motifs, respectively. The AG/TC (40.85%) and AAG (5.63%) motifs were predominant for the di- and trinucleotide repeats, respectively. Sixty-two SSR-containing ESTs were suitable for primer design. From these sequences, 23 EST-SSR markers were developed and were applied to 39 cultivated varieties of N. nucifera, 10 accessions of wild N. nucifera, and 1 accession of Nelumbo lutea (American lotus). Genetic diversity and genetic relationships were examined by constructing unweighted pair-group method with arithmetic average dendrograms and principal coordinates analysis plots based on SSR polymorphisms. Results indicated genetic differentiation between cultivated and wild lotus and between seed lotus cultivars and rhizome lotus cultivars. These EST-SSR markers will be useful for further studies of the evolution and diversity of Nelumbo.

Updated foxtail millet genome assembly and gene mapping of nine key agronomic traits by resequencing a RIL population

Abstract Foxtail millet (Setaria italica) provides food and fodder in semi-arid regions and infertile land. Resequencing of 184 foxtail millet recombinant inbred lines (RILs) was carried out to aid essential research on foxtail millet improvement. A total 483 414 single nucleotide polymorphisms were determined. Bin maps were constructed based on the RILs’ recombination data. Based on the high-density bin map, we updated Zhanggu reference with 416 Mb after adding 16 Mb unanchored scaffolds and Yugu reference with some assembly error correction and 3158 gaps filled. Quantitative trait loci (QTL) mapping of nine agronomic traits was done based on this RIL population, five of which were controlled by a single gene. Meanwhile, two QTLs were found for plant height, and a candidate gene showed 89% identity to the known rice gibberellin-synthesis gene sd1. Three QTLs were found for the trait of heading date. The whole genome resequencing and QTL mapping provided important tools for foxtail millet research and breeding. Resequencing of the RILs could also provide an effective way for high-quality genome assembly and gene identification.

A High Density Genetic Map Derived from RAD Sequencing and Its Application in QTL Analysis of Yield-Related Traits in Vigna unguiculata

Cowpea [Vigna unguiculata (L.) Walp.] is an annual legume of economic importance and widely grown in the semi-arid tropics. However, high-density genetic maps of cowpea are still lacking. Here, we identified 34,868 SNPs (single nucleotide polymorphisms) that were distributed in the cowpea genome based on the RAD sequencing (restriction-site associated DNA sequencing) technique using a population of 170 individuals (two cowpea parents and 168 F2:3 progenies). Of these, 17,996 reliable SNPs were allotted to 11 consensus linkage groups (LGs). The length of the genetic map was 1,194.25 cM in total with a mean distance of 0.066 cM/SNP marker locus. Using this map and the F2:3 population, combined with the CIM (composite interval mapping) method, eleven quantitative trait loci (QTL) of yield-related trait were detected on seven LGs (LG4, 5, 6, 7, 9, 10, and 11) in cowpea. These QTL explained 0.05–17.32% of the total phenotypic variation. Among these, four QTL were for pod length, four QTL for thousand-grain weight (TGW), two QTL for grain number per pod, and one QTL for carpopodium length. Our results will provide a foundation for understanding genes related to grain yield in the cowpea and genus Vigna.

Gene mapping of nine agronomic traits and genome assembly by resequencing a foxtail millet RIL population

Foxtail millet (Setaria italica) provides food and fodder in semi-arid regions and infertile land. Resequencing of 184 foxtail millet recombinant inbred lines (RILs) was carried out to aid essential research on foxtail millet improvement. Bin map were constructed based on the RILs’ recombination data. By anchoring some unseated scaffolds and filling gaps, we update two original millet reference genomes Zhanggu and Yugu to produce second editions. Gene mapping of nine agronomic traits were done based on this RIL population. The genome resequencing and QTL mapping provided important tools for foxtail millet research and breeding. Resequencing of the RILs could also provide an effective way for high quantity genome assembly and gene identification.