RNA-Seq and genetic diversity analysis of faba bean (Vicia faba L.) varieties in China.

Background: Faba bean (Vicia faba L) is one of the most important legumes in the world. However, there is relatively little genomic information available for this species owing to its large genome. The lack of data impedes the discovery of molecular markers and subsequent genetic research in faba bean. The objective of this study was to analyze the faba bean transcriptome, and to develop simple sequence repeat (SSR) markers to determine the genetic diversity of 226 faba bean varieties derived from different regions in China. Methods: Faba bean varieties with different phenotype were used in transcriptome analysis. The functions of the unigenes were analyzed using various database. SSR markers were developed and the polymorphic markers were selected to conduct genetic diversity analysis. Results: A total of 92.43 Gb of sequencing data was obtained in this study, and 133,487 unigene sequences with a total length of 178,152,541 bp were assembled. A total of 5,200 SSR markers were developed on the basis of RNA-Seq analysis. Then, 200 SSR markers were used to evaluate polymorphisms. In total, 103 (51.5%) SSR markers showed significant and repeatable bands between different faba bean varieties. Clustering analysis revealed that 226 faba bean materials were divided into five groups. Genetic diversity analysis revealed that the relationship between different faba beans in China was related, especially in the same region. These results provided a valuable data resource for annotating genes to different categories and developing SSR markers.

Comparative transcriptome analysis provides insights into grain filling commonalities and differences between foxtail millet [Setaria italica (L.) P. Beauv.] varieties with different panicle types.

Grain filling affects grain weight and quality and is among the most critical factors in determining the yield and quality of cereal crops. Though hybrids have larger panicles and numerous spikelets with a larger sink capacity than conventional varieties, data on the grain filling commonalities and differences between foxtail millet varieties with different panicle types remain sparse. In this study, we found that "Zhang Gu 13" (ZG, large panicle) exhibits a significantly higher panicle weight than "Yu Gu 18" (YG, conventional panicle) at the early stage of grain filling, but the weight of YG increased rapidly and gradually overtook ZG during the middle stages. A temporal expression pattern analysis demonstrated that the genes involved in photosynthesis, metabolic pathways, and phenylpropanoid biosynthesis were downregulated, while those related to peroxisome function, purine metabolism, and zeatin biosynthesis were upregulated during grain filling in both varieties. A total of 6,832 differentially expressed genes (DEGs) were identified in both varieties, with the majority identified at the early and late stages. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further revealed that the upregulated DEGs in YG were associated with gibberellin (GA) biosynthesis, ATP-binding cassette (ABC) transporters, and plant hormone signal transduction. Photosynthesis-related DEGs, such as photosystem and antenna proteins, were significantly upregulated in ZG. This study provides preliminary insights into the differences in gene expression and molecular mechanisms of grain filling between ZG and YG in the North China summer-sowing region.

How Does the Waterlogging Regime Affect Crop Yield? A Global Meta-Analysis.

Waterlogging, an abiotic stress, severely restricts crop yield in various parts of the world. Thus, we conducted a meta-analysis of 2,419 comparisons from 115 studies to comprehensively evaluate the overall change in crop yield induced by waterlogging in the global region. The results suggested that waterlogging obviously decreased crop yield by 32.9% on average, compared with no waterlogging, which was a result of a reduced 1,000-grain weight (13.67%), biomass (28.89%), plant height (10.68%), net photosynthetic rate (P n , 39.04%), and leaf area index (LAI, 22.89%). The overall effect of a waterlogging regime on crop yield is related to the crop type; the crop yield reduction varied between wheat (25.53%) and cotton (59.95%), with an overall average value of 36.81% under field conditions. In addition, we also found that compared with no waterlogging, waterlogging in the reproductive growth stage (41.90%) caused a greater yield reduction than in the vegetative growth stage (34.75%). Furthermore, decreases in crop yield were observed with an extension in the waterlogging duration; the greatest decreases in crop yield occurred at 15 < D ≤ 28 (53.19 and 55.96%) under field and potted conditions, respectively. Overall, the results of this meta-analysis showed that waterlogging can decrease crop yield and was mainly affected by crop type, growth stage, and experimental duration.

Field microclimate and yield for proso millet intercropping with mung bean in the dryland of Loess Plateau, Northwest China.

Based on the ecological environment features of Loess Plateau, we examined field microclimate characteristics and yield of four different intercropping patterns for proso millet (P) and mung bean (M) including 2:2, 4:2, 4:4, 2:4. The results showed that, compared with monoculture, intercropping increased plant height, leaf area index (LAI) and chlorophyll content (SPAD) of proso millet in its late growth stage, while LAI and SPAD of mung bean decreased due to the shade of the high proso millet. Mung bean appeared spindly growth for a while by increasing the plant height. Moreover, upper canopy illumination and air temperature during grain filling stage of proso millet decreased under intercropping conditions, but relative humidity substantially increased. These changes regulated soil temperature and light leakage, which decreased under intercropping systems, and thereby led to a cold and wet ecological environment. Poor atmospheric and light conditions formed a relative closure growth environment for mung bean, which suppressed its growth. The panicles, spike length, grain mass per plant and 1000-grain mass of proso millet under 2P2M, 4P2M, 4P4M and 2P4M treatments was significantly increased by 7.5%-45.0%, 2.2%-12.2%, 35.4%-94.0% and 2.3%-4.7%, respectively. This caused a 5.6%-20.7% increase of yield than the mono-culture. The branch number, pods per plant, grain mass per plant and 100-grain mass in mung bean were decreased under different intercropping treatments, and the yield was significantly reduced by 34.8%. Land equivalent ratios (LER) of each intercropping pattern were all greater than 1. Among them, LER of 2P4M was the maximum (1.86), and 2P4M treatment held relatively reasonable composite configuration. Our results suggested that 2:4 ratio of proso millet/mung bean intercropping patterns performed better than other ratios on the Loess Plateau.

[Comparison of growth and field microclimate characteristics of broomcorn millet under different fertilization conditions].

A field experiment with two broomcorn millet varieties Longmi 8 (strong drought-resistant variety) and Jinmi 4 (drought-sensitive variety) was conducted to compare their differences in growth, field microclimate and photosynthetic capacity from anthesis to maturity under different fertility conditions. The results showed that, fertilization decreased canopy temperature, air temperature, soil temperature, illumination, but improved the relative humidity among broomcorn millet plants compared with the non-fertilization treatment. With an increase of the fertilizer level, the plant height, SPAD, LAI, net photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO2 concentration in broomcorn millet showed an increasing trend, which of the high fertilization treatment were 9.2%, 15.1%, 56.6%, 17.8%, 24.6%, 14.2%, 29.7% higher than those of non-fertilization treatment, respectively. Compared with Jinmi 4, Longmi 8 showed a cold wet characteristic, with lower canopy temperature, air temperature, soil temperature; illumination, and higher plant height, LAI, SPAD and relative humidity during grain filling. Moreover, each photosynthetic index of Longmi 8 slowly decreased and extended the period of leaf photosynthetic function so as to accumulate more photosynthetic products.

[Border effect and physiological characteristics of broomcorn millet under film mulching on ridge-furrow for harvesting rainwater model in the semi-arid region of Northern Shaanxi, China].

To explore the border effect and physiological characteristic of broomcorn millet growing under different film mulching on ridge-furrow for harvesting rainwater models in the semi-arid region of Northern Shaanxi, China, a three-year field experiment was conducted with four different widths of ridge and furrow, and the bare land flat sowing as the control (NM). The width of ridge and furrow varied as ridge: furrow = 40 cm: 40 cm (P40), 60 cm: 60 cm (P60), 80 cm: 80 cm (P80), and 100 cm:100 cm (P100). The results showed that the wider the width of furrow and ridge was, the stronger the border advantage and the border effect index of the yield were. With the increase in width of furrow and ridge, the yield increasing effect of side rows increased with the maximum of 207.7%, and the yield increasing effect of middle rows decreased with the minimum of 10.3%. P60 reached the highest yield within three years. The yield contribution rate of side rows was higher than that of middle rows (P < 0.05). The chlorophyll contents, Ch1 a/Ch1 b, and photosynthetic rate of side rows were higher than those of middle rows among the different harvesting rainwater models. The wider the width of furrow and ridge was, the stronger the photosynthetic capacity of side rows was, and the weaker the photosynthetic capacity of middle rows was. The optimal type of ridge and furrow was P60 in the semi-arid region of Northern Shaanxi.

[Effects of mulching patterns on soil water, broomcorn millet growth, photosynthetic charac- teristics and yield in the dryland of Loess Plateau in China].

The objective of this study was to explore the effects of mulching patterns on soil water, growth, photosynthetic characteristics, grain yield and water use efficiency (WUE) of broomcorn millet in the dryland of Loess Plateau in China. In a three-year field experiment from 2011 to 2013, we compared four different mulching patterns with traditional plat planting (no mulching) as the control (CK). The mulching patterns included W ridge covered with common plastic film + intredune covered with straw (SG), common ridge covered with common plastic film + intredune covered with straw (LM), double ridges covered with common plastic film + intredune covered with straw (QM), and the traditional plat planting covered with straw (JG). The results showed that the soil water storage in 0-100 cm layer was significantly higher in all mulching patterns than in CK, particularly in SG then followed by LM, QM and JG, and the differences among the mulching patterns reached a significant level at the different growth stages of broomcorn millet. Among all mulching patterns, SG had the greatest effect on the growth and photosynthesis of broomcorn millet, respectively increasing the yield and WUE by 55.9% and 64.9% over CK, and the differences among the mulching patterns also reached a significant level. Therefore, SG was recommended as an efficient planting pattern for broomcorn millet production in the dryland of Loess Plateau in China.