Rice blast, caused by Magnaporthe oryzae, is a major disease of rice almost worldwide. The Chinese indica cultivar 93-11 is resistant to numerous isolates of the blast fungus in China, and can be used as broad-spectrum resistance resource, particularly in japonica rice breeding programs. In this study, we identified and mapped two blast resistance genes, Pi60(t) and Pi61(t), in cv. 93-11 using F₂ and F₃ populations derived from a cross between the susceptible cv. Lijiangxintuanheigu (LTH) and resistant cv. 93-11 and inoculated with M. oryzae isolates from different geographic origins. Pi60(t) was delimited to a 274 kb region on the short arm of chromosome 11, flanked by InDel markers K1-4 and E12 and cosegregated with InDel markers B1 and Y10. Pi61(t) was mapped to a 200 kb region on the short arm (near the centromere) of chromosome 12, flanked by InDel markers M2 and S29 and cosegregating with InDel marker M9. In the 274 kb region of Pi60(t), 93-11 contains six NBS-LRR genes including the two Pia/PiCO39 alleles (BGIOSGA034263 and BGIOSGA035032) which are quite close to the two Pia/PiCO39 alleles (SasRGA4 and SasRGA5) in Sasanishiki and CO39, with only nine amino acids differing in the protein sequences of BGIOSGA035032 and SasRGA5. In the 200 kb region of Pi61(t), 93-11 contains four NBS-LRR genes, all of which show high identities in protein sequence with their corresponding NBS-LRR alleles in susceptible cv. Nipponbare. Comparison of the response spectra and physical positions between the target genes and other R genes in the same chromosome regions indicated that Pi60(t) could be Pia/PiCO39 or its allele, whereas Pi61(t) appears to be different from Pita, Pita-2, Pi19(t), Pi39(t) and Pi42(t) in the same R gene cluster. DNA markers tightly linked to Pi60(t) and Pi61(t) will enable marker-assisted breeding and map-based cloning.

Artificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the genomic pattern surrounding it was elusive and the selection effect in that region was not clear. An association mapping panel consisting of 283 diverse modern temperate maize elite lines was genotyped by a chip containing over 55,000 evenly distributed SNPs. Ten-fold resequencing at the target region on 40 of the panel lines and 47 tropical lines was also undertaken. A genome-wide association study (GWAS) for cob glume color confirmed the P1 locus, which is located on the short arm of chromosome 1, with a − log₁₀ P value for surrounding SNPs higher than the Bonferroni threshold (α/n, α < 0.001) when a mixed linear model (MLM) was implemented. A total of 26 markers were identified in a 0.78 Mb region surrounding the P1 locus, including 0.73 Mb and 0.05 Mb upstream and downstream of the P1 gene, respectively. A clear linkage disequilibrium (LD) block was found and LD decayed very rapidly with increasing physical distance surrounding the P1 locus. The estimates of π and Tajima's D were significantly (P < 0.001) lower at both ends compared to the locus. Upon comparison of temperate and tropical lines at much finer resolution by resequencing (180-fold finer than chip SNPs), a more structured LD block pattern was found among the 40 resequenced temperate lines. All evidence indicates that the P1 locus in temperate maize has not undergone neutral evolution but has been subjected to artificial selection during post-domestication selection or improvement. The information and analytical results generated in this study provide insights as to how breeding efforts have affected genome evolution in crop plants.

Genetic diversity, population structure, and genome-wide marker-trait association analyses were conducted on a special collection of 298 homozygous lettuce (Lactuca sativa L.) lines. Each of these lines was derived from a single plant that had been genotyped with 384 SNP markers using LSGermOPA. They included 122 butterhead, 53 romaine, 63 crisphead, 53 leaf and 7 stem types. Genetic diversity among these plants was assessed by pairwise comparison based on 322 high-quality SNP markers selected from 384 SNPs. Only 258 unique genotypes were identified among the 298 lines because 26 pairs or small groups (a total of 66 lines) shared identical genotypes. The average genetic similarity coefficient (GS) among these unique genotypes was 63.9% with a range of 40.6% to 99.8%. A phylogenetic tree was constructed based on the genotypic data. The most likely number of populations was estimated to be two or six. Association analysis between the 322 SNP markers and 10 phenotypic traits using the 258 homozygous lines was performed by three different methods: single factor analysis, general linear model analysis, and mixed linear model analysis. Nine significant marker-trait associations (SMTAs) were detected at P < 0.0001 with all three methods and also when considering kinship and/or population structure for this collection, with five SMTAs for seed coat color, one for leaf undulation, two for leaf anthocyanin, and one for stem anthocyanin. These markers will be useful in marker-assisted selection after further validation with segregating populations.

Oil, protein and starch are key chemical components of maize kernels. A population of 245 recombinant inbred lines (RILs) derived from a cross between a high-oil inbred line, By804, and a regular inbred line, B73, was used to dissect the genetic interrelationships among oil, starch and protein content at the individual QTL level by unconditional and conditional QTL mapping. Combined phenotypic data over two years with a genetic linkage map constructed using 236 markers, nine, five and eight unconditional QTL were detected for oil, protein and starch content, respectively. Some QTL for oil, protein and starch content were clustered in the same genomic regions and the direction of their effects was consistent with the sign of their correlation. In conditional QTL mapping, 37 (29/8) unconditional QTL were not detected or showed reduced effects, four QTL demonstrated similar effects under unconditional and conditional QTL mapping, and 17 additional QTL were identified by conditional QTL mapping. These results imply that there is a strong genetic relationship among oil, protein and starch content in maize kernels. The information generated in the present investigation could be helpful in marker-assisted breeding for maize varieties with desirable kernel quality traits.

Anatomical and chemical characteristics of stems affect lodging in wheat (Triticum aestivum L.) cultivars. Traits associated with lodging resistance, such as plant height, stem strength, culm wall thickness, pith diameter, and stem diameter, were extensively investigated in earlier studies. However, the solid stem trait was rarely considered. In this study, we measured a range of anatomical and chemical characteristics on solid and hollow stemmed wheat cultivars. Significant correlations were detected between resistance to lodging and several anatomical features, including width of mechanical tissue, weight of low internodes, and width of stem walls. Morphological features that gave the best indication of improved lodging resistance were increased stem width, width of mechanical tissue layer, and stem density. Multiple linear regression analysis showed that 99% of the variation in lodging resistance could be explained by the width of the mechanical tissue layer, suggesting that solid stemmed wheat has several anatomical features for increasing resistance to lodging. In addition, microsatellite markers GWM247 and GWM340 were linked to a single solid stem QTL on chromosome 3BL in a population derived from the cross Xinongshixin (solid stem)/Line 3159 (hollow stem). These markers should be valuable in breeding wheat for solid stem.

Aphids are major agricultural pests that cause significant yield losses in crop plants each year. (E)-β-farnesene (EβF) is the main or only component of an alarm pheromone involved in chemical communication within aphid species and particularly in the avoidance of predation. EβF also occurs in the essential oil of some plant species, and is catalyzed by EβF synthase. By using oligonucleotide primers designed from the known sequence of an EβF synthase gene from black peppermint (Mentha × piperita), two cDNA sequences, MaβFS1 and MaβFS2, were isolated from Asian peppermint (Mentha asiatica). Expression pattern analysis showed that the MaβFS1 gene exhibited higher expression in flowers than in roots, stems and leaves at the transcriptional level. Overexpression of MaβFS1 in tobacco plants resulted in emission of pure EβF ranging from 2.62 to 4.85 ng d^{− 1} g^{− 1} of fresh tissue. Tritrophic interactions involving peach aphids (Myzus persicae), and predatory lacewing (Chrysopa septempunctata) larvae demonstrated that transgenic tobacco expressing MaβFS1 had lower aphid infestation. This result suggested that the EβF synthase gene from Asian peppermint could be a good candidate for genetic engineering of agriculturally important crop plants.

Fusarium verticillioides was labeled with DsRed via Agrobacterium tumefaciens-mediated transformation to examine differences in colonization and reactions of resistant and susceptible inbred lines of maize (Zea mays L.). The extent of systemic colonization of F. verticillioides in roots from maize lines either resistant or susceptible to the fungus was studied by visualizing the red fluorescence produced by the fungus expressing DsRed. The difference in quantities of colony forming units (CFU) in roots and basal stems, production of fumonisin B1, and pH of root were determined. Although F. verticillioides colonized both resistant and susceptible lines, differences were observed in the pattern and extent of fungal colonization in the two types of maize lines. The fungus colonized the susceptible lines producing mosaic patterns by filling the individual root cells with hyphae. Such a pattern of colonization was rarely observed in resistant lines, which were less colonized by the fungus than the susceptible lines in terms of CFUs. The production of mycotoxin fumonisin B1 in roots from different lines was closely correlated with the amount of F. verticillioides colonization, rather than the pH or amylopectin concentrations in the root. The findings from this study contribute to a better understanding of the defense mechanism in resistant maize lines to F. verticillioides.

Grain weight is a key determinant of grain yield in rice. Three sets of rice populations with overlapping segregating regions in isogenic backgrounds were established in the generations of BC₂F₅, BC₂F₆ and BC₂F₇, derived from Zhenshan 97 and Milyang 46, and used for dissection of quantitative trait loci (QTL) for grain weight. Two QTL linked in repulsion phase on the long arm of chromosome 1 were separated. One was located between simple sequence repeat (SSR) markers RM11437 and RM11615, having a smaller additive effect with the enhancing allele from the maintainer line Zhenshan 97 and a partially dominant effect for increasing grain weight. The other was located between SSR markers RM11615 and RM11800, having a larger additive effect with the enhancing allele from the restorer line Milyang 46 and a partially dominant effect for increasing grain weight. When the two QTL segregated simultaneously, a residual additive effect with the enhancing allele from Milyang 46 and an over-dominance effect for increasing grain weight were detected. This suggests that dominant QTL linked in repulsion phase might play an important role in heterosis in rice. Our study also indicates that the use of populations with overlapping segregating regions in isogenic backgrounds is helpful for the dissection of minor linked QTL.

The objective of this study was to understand the effects of plant spacing on grain yield and root competition in summer maize (Zea mays L.). Maize cultivar Denghai 661 was planted in rectangular tanks (0.54 m × 0.27 m × 1.00 m) under 27 cm (normal) and 6 cm (narrow) plant spacing and treated with zero and 7.5 g nitrogen (N) per plant. Compared to normal plant spacing, narrow plant spacing generated less root biomass in the 0-20 cm zone under both N rates, slight reductions of dry root weight in the 20-40 cm and 40-70 cm zones at the mid-grain filling stage, and slight variation of dry root weights in the 70-100 cm zone during the whole growth period. Narrow plant spacing decreased root reductive activity in all root zones, especially at the grain-filling stage. Grain yield and above-ground biomass were 5.0% and 8.4% lower in the narrow plant spacing than with normal plant spacing, although narrow plant spacing significantly increased N harvest index and N use efficiency in both grain yield and biomass, and higher N translocation rates from vegetative organs. These results indicate that the reductive activity of maize roots in all soil layers and dry weights of shallow roots were significantly decreased under narrow plant spacing conditions, resulting in lower root biomass and yield reduction at maturity. Therefore, a moderately dense sowing is a basis for high yield in summer maize.

The components and contents of high-molecular-weight glutenin subunits (HMW-GS) in wheat grains affect glutenin macropolymer (GMP) size, which is considered an important flour quality trait in wheat. Four wheat cultivars (Shiluan 02-1, Yannong 24, Jinan 17 and Lumai 21) with different end-use qualities were used to investigate the HMW-GS and GMP contents, and the GMP particle distributions in grain produced under irrigated and rainfed conditions. The percent volume of GMP particles and the contents of HMW-GS and GMP were affected by genotype and soil water. Genotype × soil water interaction was significant only for GMP particles < 12 μm and > 100 μm in the growing season of 2010-2011. Irrigated and rainfed conditions had different influences on the GMP particle distribution in the four cultivars. Compared to irrigated treatment, the rainfed treatment had higher accumulations of HMW-GS and GMP, especially in cultivars Yannong 24, Jinan 17 and Lumai 21. Rainfed conditions also increased the proportion of large size particles of GMP, indicating that different water regimes had an effect on grain quality. According to correlation coefficients (r), the contents of HMW-GS and GMP in grains were negatively correlated with the volume of < 12 μm GMP particles, but positively correlated with GMP particles > 100 μm.