Roots are a vital organ for absorbing soil moisture and nutrients and influence drought resistance. The identification of quantitative trait loci (QTLs) with molecular markers may allow the estimation of parameters of genetic architecture and improve root traits by molecular marker-assisted selection (MAS). A mapping population of 120 recombinant inbred lines (RILs) derived from a cross between japonica upland rice 'IRAT109' and paddy rice 'Yuefu' was used for mapping QTLs of developmental root traits. All plant material was grown in PVC-pipe. Basal root thickness (BRT), root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW) and root volume (RV) were phenotyped at the seedling (I), tillering (II), heading (III), grain filling (IV) and mature (V) stages, respectively. Phenotypic correlations showed that BRT was positively correlated to MRL at the majority of stages, but not correlated with RN. MRL was not correlated to RN except at the seedling stage. BRT, MRL and RN were positively correlated to RFW, RDW and RV at all growth stages. QTL analysis was performed using QTLMapper 1.6 to partition the genetic components into additive-effect QTLs, epistatic QTLs and QTL-by-year interactions (Q x E) effect. The results indicated that the additive effects played a major role for BRT, RN and MRL, while for RFW, RDW and RV the epistatic effects showed an important action and Q x E effect also played important roles in controlling root traits. A total of 84 additive-effect QTLs and 86 pairs of epistatic QTLs were detected for the six root traits at five stages. Only 12 additive QTLs were expressed in at least two stages. This indicated that the majority of QTLs were developmental stage specific. Two main effect QTLs, brt9a and brt9b, were detected at the heading stage and explained 19% and 10% of the total phenotypic variation in BRT without any influence from the environment. These QTLs can be used in breeding programs for improving root traits.

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Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most devastating diseases in common wheat (Triticum aestivum L.) worldwide. The objectives of this study were to map a stripe rust resistance gene in Chinese wheat cultivar Chuanmai 42 using molecular markers and to investigate its allelism with Yr24 and Yr26. A total of 787 F2 plants and 186 F3 lines derived from a cross between resistant cultivar Chuanmai 42 and susceptible line Taichung 29 were used for resistance gene tagging. Also 197 F2 plants from the cross Chuanmai 42xYr24/3*Avocet S and 726 F2 plants from Chuanmai 42xYr26/3*Avocet S were employed for allelic test of the resistance genes. In all, 819 pairs of wheat SSR primers were used to test the two parents, as well as resistant and susceptible bulks. Subsequently, nine polymorphic markers were employed for genotyping the F2 and F3 populations. Results indicated that the stripe rust resistance in Chuanmai 42 was conferred by a single dominant gene, temporarily designated YrCH42, located close to the centromere of chromosome 1B and flanked by nine SSR markers Xwmc626, Xgwm273, Xgwm11, Xgwm18, Xbarc137, Xbarc187, Xgwm498, Xbarc240 and Xwmc216. The resistance gene was closely linked to Xgwm498 and Xbarc187 with genetic distances of 1.6 and 2.3 cM, respectively. The seedling tests with 26 PST isolates and allelic tests indicated that YrCH42, Yr24 and Yr26 are likely to be the same gene.

A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding.

In flowering plants, pollen formation depends on the differentiation and interaction of two cell types in the anther: the reproductive cells, called microsporocytes, and somatic cells that form the tapetum. Previously, we cloned a pollen specific gene, zm401, from a cDNA library generated from the mature pollen of Zea mays. Expression of partial cDNA of zm401 in maize and ectopic expression of zm401 in tobacco suggested it may play a role in anther development. Here we present the expression and functional characterization of this pollen specific gene in maize. Zm401 is expressed primarily in the anthers (tapetal cells as well as microspores) in a developmentally regulated manner. That is, it is expressed from floret forming stage, increasing in concentration up to mature pollen. Knockdown of zm401 significantly affected the expression of ZmMADS2, MZm3-3, and ZmC5, critical genes for pollen development; led to aberrant development of the microspore and tapetum, and finally male-sterility. Zm401 possesses highly conserved sequences and evolutionary conserved stable RNA secondary structure in monocotyledon. These data show that zm401 could be one of the key growth regulators in anther development, and functions as a short-open reading-frame mRNA (sORF mRNA) and/or noncoding RNA (ncRNA).

Fusarium wilt (FW), caused by the soilborne fungus Fusarium oxysporum f. sp. vasinfectum (FOV), with eight races recognized, is one of the most destructive diseases in cotton (Gossypium spp.). Employment of FW‐resistant cultivars has proven to be the most cost‐effective method to control the disease. This review provides a comprehensive synthesis of research progress in breeding, genetics, and molecular mapping of FW resistance. A focused pedigree analysis in Upland cotton (G. hirsutum L.) has identified five major FW‐resistant sources (‘Dillon’, ‘Dixie Triumph’, ‘Cook 307‐6’, ‘Coker Clevewilt’, and ‘Wild’) in the United States and three (‘Chuan 52‐128’, ‘Chuan 57‐681’, and ‘CRI 12’) in China. The use of numerous early segregating populations has consistently confirmed the predominant presence of additive gene effects on FW resistance; however, heritability is usually low because of high experimental error. Several mapping studies have detected approximately 40 quantitative trait loci (QTL) on 19 chromosomes. A number of qualitative genetic studies have identified five major resistance genes in Upland and Pima (G. barbadense L.) cotton including Fw1, Fw2, FwR (chromosome 17), FOV1 (chromosome 16), and FOV4 (chromosome 14). There are other major resistance genes identified through marker or segregating analysis, but methods with high and uniform infection by FOV are required to confirm the results. More differential hosts should be developed to differentiate new races, and more resistance genes from new sources should be identified for their strategic deployment in preventing a possible risk of disease epidemic.

BackgroundGossypium barbadense (Sea Island, Egyptian or Pima cotton) cotton has high fiber quality, however, few studies have investigated the genetic basis of its traits using molecular markers. Genome complexity reduction approaches such as genotyping-by-sequencing have been utilized to develop abundant markers for the construction of high-density genetic maps to locate quantitative trait loci (QTLs).ResultsThe Chinese G. barbadense cultivar 5917 and American Pima S-7 were used to develop a recombinant inbred line (RIL) population with 143 lines. The 143 RILs together with their parents were tested in three replicated field tests for lint yield traits (boll weight and lint percentage) and fiber quality traits (fiber length, fiber elongation, fiber strength, fiber uniformity and micronaire) and then genotyped using GBS to develop single-nucleotide polymorphism (SNP) markers. A high-density genetic map with 26 linkage groups (LGs) was constructed using 3557 GBS SNPs spanning a total genetic distance of 3076.23 cM at an average density of 1.09 cM between adjacent markers. A total of 42 QTLs were identified, including 24 QTLs on 12 LGs for fiber quality and 18 QTLs on 7 LGs for lint yield traits, with LG1 (9 QTLs), LG10 (7 QTLs) and LG14 (6 QTLs) carrying more QTLs. Common QTLs for the same traits and overlapping QTLs for different traits were detected. Each individual QTLs explained 0.97 to 20.7% of the phenotypic variation.ConclusionsThis study represents one of the first genetic mapping studies on the fiber quality and lint yield traits in a RIL population of G. barbadense using GBS-SNPs. The results provide important information for the subsequent fine mapping of QTLs and the prediction of candidate genes towards map-based cloning and marker-assisted selection in cotton.

Sea-island cotton (Gossypium barbadense) has drawn great attention in the textile industry for its comprehensive resistance and superior fiber properties. However, the mechanisms involved in fiber growth and development are unclear. As TCP transcription factors play important roles in plant growth and development, this study investigated the TCP family genes in G. barbadense (GbTCP). We identified 75 GbTCP genes, of which 68 had no introns. Phylogenetic analyses categorized the GbTCP transcription factors into 11 groups. Genomic analyses showed that 66 genes are located on 21 chromosomes. Phylogenetic analyses of G. arboreum, G. raimondii, G. hirsutum, G. barbadense, Theobroma cacao, Arabidopsis thaliana, Oryza sativa, Sorghum bicolor, and Zea mays, Picea abies, Sphagnum fallax and Physcomitrella patens, categorized 373 TCP genes into two classes (Classes I and II). By studying the structures of TCP genes in sea-island cotton, we identified genes from the same evolutionary branches that showed similar motif patterns. qRT-PCR results suggested that the GbTCPs had different expression patterns in fibers at various developmental stages of cotton, with several showing specific expression patterns during development. This report helps lay the foundation for future investigations of TCP functions and molecular mechanisms in sea-island cotton fiber development.