The identification of stable quantitative trait locus (QTL) for yield-related traits and tightly linked molecular markers is important for improving wheat grain yield. In the present study, six yield-related traits in a recombinant inbred line (RIL) population derived from the Zhongmai 578/Jimai 22 cross were phenotyped in five environments. The parents and 262 RILs were genotyped using the wheat 50K single nucleotide polymorphism (SNP) array. A high-density genetic map was constructed with 1 501 non-redundant bin markers, spanning 2 384.95 cM. Fifty-three QTLs for six yield-related traits were mapped on chromosomes 1D (2), 2A (9), 2B (6), 2D, 3A (2), 3B (2), 4A (5), 4D, 5B (8), 5D (2), 7A (7), 7B (3) and 7D (5), which explained 2.7–25.5% of the phenotypic variances. Among the 53 QTLs, 23 were detected in at least three environments, including seven for thousand-kernel weight (TKW), four for kernel length (KL), four for kernel width (KW), three for average grain filling rate (GFR), one for kernel number per spike (KNS) and four for plant height (PH). The stable QTLs QKl.caas-2A.1, QKl.caas-7D, QKw.caas-7D, QGfr.caas-2B.1, QGfr.caas-4A, QGfr.caas-7A and QPh. caas-2A.1 are likely to be new loci. Six QTL-rich regions on 2A, 2B, 4A, 5B, 7A and 7D, showed pleiotropic effects on various yield traits. TaSus2-2B and WAPO-A1 are potential candidate genes for the pleiotropic regions on 2B and 7A, respectively. The pleiotropic QTL on 7D for TKW, KL, KW and PH was verified in a natural population. The results of this study enrich our knowledge of the genetic basis underlying yield-related traits and provide molecular markers for high-yield wheat breeding.

With the development of sequencing technology, insertions-deletions (InDels) have been increasingly reported to be involved in the genetic deter mination of agronomical traits.  However, most studies have focused on the identification and application of short-InDels (1–15 bp) for genetic analysis.  The objective of this study was to deeply deploy long-InDels (>15 bp) for the genetic analysis of important agronomic traits in soybean.  A total of 13 573 polymorphic long-InDels were identified between parents Zhongpin 03-5373 (ZP) and Zhonghuang 13 (ZH), which were unevenly distributed on 20 chromosomes of soybean, varying from 321 in Chr11 to 1 246 in Chr18.  Consistent with the distribution pattern of annotated genes, the average density of long-InDels in arm regions was significantly higher than that in pericentromeric regions at the P=0.01 level.  A total of 2 704 (19.9% of total) long-InDels were located in genic regions, including 319 large-effect long-InDels, which resulted in truncated or elongated protein sequences.  A previously identified QTL (qPH16) underlying plant height was further analyzed, and it was found that 26 out of 35 (74.3%) long-InDel markers located in the qPH16 region showed clear polymorphisms between parents ZP and ZH.  Seven markers, including three long-InDels and four previously reported SNP markers, were used to genotype 242 recombinant inbred lines derived from ZP×ZH.  As a result, the qPH16 locus was narrowed from a 960-kb region to a 477.55-kb region, containing 65 annotated genes.  Therefore, these long-InDels are a complementary genetic resource of SNPs and short-InDels for plant height and can facilitate genetic studies and molecular assisted selection breeding in soybean.

Plant height is an important agronomic trait, which is governed by multiple genes with major or minor effects.  Of numerous QTLs for plant height reported in soybean, most are in large genomic regions, which results in a still unknown molecular mechanism for plant height.  Increasing the density of molecular markers in genetic maps will significantly improve the efficiency and accuracy of QTL mapping.  This study constructed a high-density genetic map using 4 011 recombination bin markers developed from whole genome re-sequencing of 241 recombinant inbred lines (RILs) and their bi-parents, Zhonghuang 13 (ZH) and Zhongpin 03-5373 (ZP).  The total genetic distance of this bin map was 3 139.15 cM, with an average interval of 0.78 cM between adjacent bin markers.  Comparative genomic analysis indicated that this genetic map showed a high collinearity with the soybean reference genome.  Based on this bin map, nine QTLs for plant height were detected across six environments, including three novel loci (qPH-b_11, qPH-b_17 and qPH-b_18).  Of them, two environmentally stable QTLs qPH-b_13 and qPH-b_19-1 played a major role in plant height, which explained 10.56–32.7% of the phenotypic variance.  They were fine-mapped to 440.12 and 237.06 kb region, covering 54 and 28 annotated genes, respectively.  Via the function of homologous genes in Arabidopsis and expression analysis, two genes of them were preferentially predicted as candidate genes for further study.

Changes in the soil nematode community induced by global warming may have a considerable influence on agro-ecosystem functioning. However, the impacts of predicted warming on nematode community in farmland (e.g., winter wheat field) have not been well documented. Therefore, a field experiment with free air temperature increase (FATI) was conducted to investigate the responses of the soil nematode community to nighttime warming in a winter wheat field of Yangtze Delta Plain, China, during 2007 to 2009. Nighttime warming (NW) by 1.8°C at 5-cm soil depth had no significant impact on the total nematode abundance compared to un-warmed control (CK). However, NW significantly affected the nematode community structure. Warming favored the bacterivores and fungivores, such as Acrobeles, Monhystera, Rhabditis, and Rhabdontolaimus in bacterivores, and Filenchus in fungivores, while the plant-parasites were hindered, such as Helicotylenchus and Psilenchus. Interestingly, the carnivores/ omnivores remained almost unchanged. Hence, the abundances of bacterivores and fungivores were significantly higher under NW than those under CK. Similarly, the abundances of plant-parasites were significantly lower under NW than under CK. Furthermore, Wasilewska index of the nematode community was significantly higher under NW than those under CK, indicating beneficial effect to the plant in the soil. Our results suggest that nighttime warming may improve soil fertility and decrease soil- borne diseases in winter wheat field through affecting the soil nematode community. It is also indicated that nighttime warming may promote the sustainability of the nematode community by altering genera-specific habitat suitability for soil biota.

Macroscopic grasp of agricultural carbon emissions status, spatial-temporal characteristics as well as driving factors are the basic premise in further research on China’s agricultural carbon emissions. Based on 23 kinds of major carbon emission sources including agricultural materials inputs, paddy field, soil and livestock breeding, this paper firstly calculated agricultural carbon emissions from 1995 to 2010, as well as 31 provinces and cities in 2010 in China. We then made a decomposed analysis to the driving factors of carbon emissions with logarithmic mean Divisia index (LMDI) model. The results show: (1) The amount of agricultural carbon emissions is 291.1691 million t in 2010. Compared with 249.5239 million t in 1995, it increased by 16.69%, in which, agricultural materials inputs, paddy field, soil, enteric fermentation, and manure management accounted for 33.59, 22.03, 7.46, 17.53 and 19.39% of total agricultural carbon emissions, respectively. Although the amount exist ups and downs, it shows an overall trend of cyclical rise; (2) There is an obvious difference among regions: the amount of agricultural carbon emissions from top ten zones account for 56.68%, while 9.84 % from last 10 zones. The traditional agricultural provinces, especially the major crop production areas are the main source regions. Based on the differences of carbon emission rations, 31 provinces and cities are divided into five types, namely agricultural materials dominant type, paddy field dominant type, enteric fermentation dominant type, composite factors dominant type and balanced type. The agricultural carbon emissions intensity in west of China is the highest, followed by the central region, and the east zone is the lowest; (3) Compared with 1995, efficiency, labor and structure factors cut down carbon emissions by 65.78, 27.51 and 3.19%, respectively; while economy factor increase carbon emissions by 113.16%.

Phosphorus (P) is one of the three primary macronutrients that are required in large amounts for plant growth and development. To better understand molecular mechanism of maize and identify relevant genes in response to phosphorus deficiency, we used Solexa/Illumina’s digital gene expression (DGE) technology to investigate six genome-wide expression profiles of seedling roots of the low-P tolerant maize inbred line 178. DGE studies were conducted at 6, 24 and 72 h under both phosphorus deficient and sufficient conditions. Approximately 3.93 million raw reads for each sample were sequenced and 6 816 genes exhibited significant levels of differential expressions in at least one of three time points in response to P starvation. The number of genes with increased expression increased over time from 6 to 24 h, whereas genes with decreased expression were more abundant at 72 h, suggesting a gradual response process for P deficiency at different stages. Gene annotations illustrated that most of differentially expressed genes (DEGs) are involved in different cellular and molecular processes such as environmental adaptation and carbohydrate metabolism. The expression of some known genes identified in other plants, such as those involved in root architecture, P metabolism and transport were found to be altered at least two folds, indicating that the mechanisms of molecular and morphological adaptation to P starvation are conserved in plants. This study provides insight into the general molecular mechanisms underlying plant adaptation to low-P stress and thus may facilitate molecular breeding for improving P utilization in maize.

Large grain is a favorable trait for appearance quality and large sink potential in wheat breeding.  A stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from the cross of Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895).  Here, a BC₁F₆ residual heterozygous line was selected from the cross of ZM871/ZM895//ZM871 population, and six heterozygous recombinant plants were identified in the BC₁F₇ population from self-pollination of the heterozygous line.  QGl.caas-5BS was delimited into an interval of approximately 2.2 Mb flanked by markers Kasp_5B33 and Kasp_5B2 (25.3-27.5 Mb) through phenotyping and genotyping the secondary mapping populations derived from these heterozygous recombinant plants.  Five genes were predicted as candidates of QGl.caas-5BS based on sequence polymorphism and differential expression analyses.  Further mutation analysis showed that TraesCS5B02G026800 is likely the causal gene of QGl.caas-5BS.  A gene-specific marker Kasp_5B_Gl for TraesCS5B02G026800 was developed, and a significant genetic effect of QGl.caas-5BS on grain length was identified in a validation population including 166 cultivars using the marker.  These findings lay a good foundation for map-based cloning of QGl.caas-5BS and provide a breeding-applicable marker for the improvement of grain length in wheat.