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Gao L.,Institute of Crop Science | Zhao G.,Institute of Crop Science | Huang D.,CAS Beijing Institute of Genomics | Jia J.,Institute of Crop Science
Scientific Reports | Year: 2017

Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions. This study will not only help future wheat breeding and evolutionary studies, but will also accelerate study of other crops, especially polyploids. © The Author(s) 2017.


Li H.,Institute of Crop Science | Li H.,Chinese Academy of Agricultural Sciences | Singh R.P.,International Maize and Wheat Improvement Center | Braun H.-J.,International Maize and Wheat Improvement Center | And 3 more authors.
Crop Science | Year: 2013

Doubled haploid (DH) technology has been used in breeding programs for several decades and is currently the method of choice in a number of crop species, including barley (Hordeum vulgare L.), rapeseed (Brassica napus L.), maize (Zea mays L.), and wheat (Triticum aestivum L.). In this study we investigated via computer simulation the benefit of using DHs compared with the conventional wheat breeding strategy used at CIMMYT. Two strategies using DHs were considered: DH lines directly derived from F1 hybrids (F1-DH), and DH lines derived from F3 individuals that are retained following selection for agronomic traits in the F2 generation (F3-DH). Genetic gains per cycle, per year, and per dollar spent were consistently higher for conventional breeding than for DH breeding strategies, especially gains per dollar. Though the F1-DH strategy saved 1 yr in completing a breeding cycle, genetic gains per year for the adaptation trait from F1-DH were much lower than those from conventional breeding, where two growing seasons are used per year. Though the DH breeding strategy showed no significant advantages over the conventional wheat shuttlebreeding regime of CIMMYT, we did not exclude the possibility that the DH breeding strategy may have advantages when genetic gains per unit of time are considered, and only one generation is grown per year. The conventional shuttle regime will continue to be the major wheat breeding strategy at CIMMYT, where two cycles can be grown per year and breeders can do selection in large populations in both cycles. © Crop Science Society of America.


Song S.,Institute of Crop Science | Hou W.,Institute of Crop Science | Godo I.,Migal Galilee Technology Center | Wu C.,Institute of Crop Science | And 7 more authors.
Journal of Experimental Botany | Year: 2013

Soybean seeds provide an excellent source of protein for human and livestock nutrition. However, their nutritional quality is hampered by a low concentration of the essential sulfur amino acid, methionine (Met). In order to study factors that regulate Met synthesis in soybean seeds, this study used the Met-insensitive form of Arabidopsis cystathionine γ-synthase (AtD-CGS), which is the first committed enzyme of Met biosynthesis. This gene was expressed under the control of a seed-specific promoter, legumin B4, and used to transform the soybean cultivar Zigongdongdou (ZD). In three transgenic lines that exhibited the highest expression level of AtD-CGS, the level of soluble Met increased significantly in developing green seeds (3.8-7-fold). These seeds also showed high levels of other amino acids. This phenomenon was more prominent in two transgenic lines, ZD24 and ZD91. The total Met content, which including Met incorporated into proteins, significantly increased in the mature dry seeds of these two transgenic lines by 1.8- and 2.3-fold, respectively. This elevation was accompanied by a higher content of other protein-incorporated amino acids, which led to significantly higher total protein content in the seeds of these two lines. However, in a third transgenic line, ZD01, the level of total Met and the level of other amino acids did not increase significantly in the mature dry seeds. This line also showed no significant change in protein levels. This suggests a positive connection between high Met content and the synthesis of other amino acids that enable the synthesis of more seed proteins. © The Author [2013].


Vari E.,Institute of Crop Science | Pepo P.,Institute of Crop Science
WIT Transactions on Ecology and the Environment | Year: 2014

This research focused on the effects of previous crop, fertilization and irrigation on the Leaf Area Index (LAI) and relative chlorophyll content (SPAD) of maize and the amount of yield in three different crop years. We were also looking for the relations between these parameters. As an average of the three years, the year, the crop rotation, the irrigation and the fertilization had a 3.5%, 29.8%, 21.5% and 45.2% share in the yield, respectively. The maximum SPAD-values were measured at tasseling and silking periods depending upon the year. In all three crop rotation models, significant differences were found between the control and the fertilization levels of N120-180+PK. As a result of irrigation, an increasing trend can be observed in the SPAD. The maximum LAI were measured at the 12-leaf or tassel depending on the period of the year. The dynamics and maximum value of the LAI were significantly determined by fertilization. Crop rotation had a strong effect, though it varied with the year. There were no significant differences in leaf area between the irrigated and the non-irrigated treatments. The fertilization had the strongest impact (r = 0.533–0.723) on yield among the agrotechnical elements. The correlation between the crop rotation and the yield was significant but weak (r = 0.336–0.423), while irrigation had a loose, non-significant correlation with yield in 2011 and 2012. In 2013, irrigation had a greater influence on the yield than in 2011 and 2012 (r = 0.497). © 2014 WIT Press.


Wu J.,Institute of Crop Science | Wang L.,Institute of Crop Science | Li L.,Institute of Crop Science | Wang S.,Chinese Academy of Agricultural Sciences
PLoS ONE | Year: 2014

The common bean (Phaseolus vulgaris L.) is one of the most important food legumes, far ahead of other legumes. The average grain yield of the common bean worldwide is much lower than its potential yields, primarily due to drought in the field. However, the gene network that mediates plant responses to drought stress remains largely unknown in this species. The major goals of our study are to identify a large scale of genes involved in drought stress using RNA-seq. First, we assembled 270 million high-quality trimmed reads into a non-redundant set of 62,828 unigenes, representing approximately 49 Mb of unique transcriptome sequences. Of these unigenes, 26,501 (42.2%) common bean unigenes had significant similarity with unigenes/predicted proteins from other legumes or sequenced plants. All unigenes were functionally annotated within the GO, COG and KEGG pathways. The strategy for de novo assembly of transcriptome data generated here will be useful in other legume plant transcriptome studies. Second, we identified 10,482 SSRs and 4,099 SNPs in transcripts. The large number of genetic markers provides a resource for gene discovery and development of functional molecular markers. Finally, we found differential expression genes (DEGs) between terminal drought and optimal irrigation treatments and between the two different genotypes Long 22-0579 (drought tolerant) and Naihua (drought sensitive). DEGs were confirmed by quantitative real-time PCR assays, which indicated that these genes are functionally associated with the drought-stress response. These resources will be helpful for basic and applied research for genome analysis and crop drought resistance improvement in the common bean. © 2014 Wu et al.


Hori K.,Institute of Crop Science | Matsubara K.,Institute of Crop Science | Yano M.,Institute of Crop Science
Theoretical and Applied Genetics | Year: 2016

Key message: Integration of previous Mendelian genetic analyses and recent molecular genomics approaches, such as linkage mapping and QTL cloning, dramatically strengthened our current understanding of genetic control of rice flowering time.Abstract: Flowering time is one of the most important agronomic traits for seed production in rice (Oryza sativa L.). It is controlled mainly by genes associated with photoperiod sensitivity, particularly in short-day plants such as rice. Since the early twentieth century, rice breeders and researchers have been interested in elucidating the genetic basis of flowering time because its modification is important for regional adaptation and yield optimization. Although flowering time is a complex trait controlled by many quantitative trait loci (QTLs), classical genetic studies have shown that many associated genes are inherited in accordance with Mendelian laws. Decoding the rice genome sequence opened a new era in understanding the genetic control of flowering time on the basis of genome-wide mapping and gene cloning. Heading date 1 (Hd1) was the first flowering time QTL to be isolated using natural variation in rice. Recent accumulation of information on rice genome has facilitated the cloning of other QTLs, including those with minor effects on flowering time. This information has allowed us to rediscover some of the flowering genes that were identified by classical Mendelian genetics. The genes characterized so far, including Hd1, have been assigned to specific photoperiod pathways. In this review, we provide an overview of the studies that led to an in-depth understanding of the genetic control of flowering time in rice, and of the current state of improving and fine-tuning this trait for rice breeding. © 2016 Springer-Verlag Berlin Heidelberg


ZHOU G.-a.,Institute of Crop science | QIU L.-j.,Institute of Crop science
Agricultural Sciences in China | Year: 2010

The Cl- homeostasis was known as the major mechanism of soybean to achieve NaCl tolerance, but studies on the role of chloride channel under abiotic stress were relatively few. We cloned a putative CLC-type chloride channel gene GmCLCnt from soybean via RACE and it was predicted to encode a protein of 783 amino acids with 9 possible transmembrane domains and 2 tandem CBS domains. Real-time RT-PCR analysis showed that the GmCLCnt gene was expressed in all tissues of soybean but enriched in leaves and its expression was induced by NaCl, polyethylene glycol (PEG), coldness and ABA treatments. The Arabidopsis seedlings overexpressing GmCLCnt were more tolerant to higher concentration of NaCl than those of wild type. The results suggested that the GmCLCnt may be a CLC-type chloride channel and play an important role in salt tolerance. © 2010 Chinese Academy of Agricultural Sciences.


Kovacs K.,Eötvös Loránd University | Kuzmann E.,Eötvös Loránd University | Kuzmann E.,Hungarian Academy of Sciences | Vertes A.,Eötvös Loránd University | And 4 more authors.
Plant and Soil | Year: 2010

The uptake and accumulation of iron in cucumber roots exposed to cadmium were investigated with Fe sufficient and deficient cucumber plants using Mössbauer spectroscopy, Inductively Coupled Plasma Mass Spectrometry (ICP-MS) and ferric chelate reductase activity measurements. Both Fe sufficient and Fe deficient plants were applied. In the case of Fe sufficient cucumber roots grown in nutrient solution with 10 μM Cd no changes were found in the occurrence of Fe species (mostly hydrous ferric oxides and ferric-carboxylate complexes) compared to the control where no Cd was added. In the Fe deficient roots pretreated with 0, 0.1, 1, 10 and 100 μM Cd for 3 h then supplied also with 0.5 mM 57Fe-citrate for 30 min, FeII was identified in a hexaaqua complex form. The relative amount of FeII was decreasing simultaneously with increasing Cd concentration, while the relative occurrence of FeIII species and total Fe concentration were increasing. The results support the inhibitory effect of Cd on Fe-chelate reduction. Although the reductase activity at 10 and 100 μM Cd treatment was lower than in the iron sufficient control plants, FeII could be identified by Mössbauer spectroscopy whereas in the Fe sufficient control, this form was below detection limit. These data demonstrate that the influx and the reoxidation of FeII was decreased by Cd, consequently, they refer to the competition of Cd2+ and Fe2+ during the membrane transport and the inhibition of the reoxidation process. © Springer Science + Business Media B.V. 2009.


Xu D.-B.,Northwest University, China | Xu D.-B.,Institute of Crop science | Chen M.,Institute of Crop science | Ma Y.-N.,Northwest University, China | And 5 more authors.
PLoS ONE | Year: 2015

Heterotrimeric G-proteins are versatile regulators involved in diverse cellular processes in eukaryotes. In plants, the function of G-proteins is primarily associated with ABA signaling. However, the downstream effectors and the molecular mechanisms in the ABA pathway remain largely unknown. In this study, an AGB1 mutant (agb1-2) was found to show enhanced drought tolerance, indicating that AGB1 might negatively regulate drought tolerance in Arabidopsis. Data showed that AGB1 interacted with protein kinase AtMPK6 that was previously shown to phosphorylate AtVIP1, a transcription factor responding to ABA signaling. Our study found that transcript levels of three ABA responsive genes, AtMPK6, AtVIP1 and AtMYB44 (downstream gene of AtVIP1), were significantly up-regulated in agb1-2 lines after ABA or drought treatments. Other ABA-responsive and drought-inducible genes, such as RD29A (downstream gene of AtMYB44), were also up-regulated in agb1-2 lines. Furthermore, overexpression of AtVIP1 resulted in hypersensitivity to ABA at seed germination and seedling stages, and significantly enhanced drought tolerance in transgenic plants. These results suggest that AGB1 was involved in the ABA signaling pathway and drought tolerance in Arabidopsis through down-regulating the AtMPK6, AtVIP1 and AtMYB44 cascade. © 2015 Xu et al.


PubMed | Institute of Crop Science
Type: Journal Article | Journal: PloS one | Year: 2016

Wheat is grown as a staple crop worldwide. It is important to develop an effective genotyping tool for this cereal grain both to identify germplasm diversity and to protect the rights of breeders. Single-nucleotide polymorphism (SNP) genotyping provides a means for developing a practical, rapid, inexpensive and high-throughput assay. Here, we investigated SNPs as robust markers of genetic variation for typing wheat cultivars. We identified SNPs from an array of 9000 across a collection of 429 well-known wheat cultivars grown in China, of which 43 SNP markers with high minor allele frequency and variations discriminated the selected wheat varieties and their wild ancestors. This SNP-based barcode will allow for the rapid and precise identification of wheat germplasm resources and newly released varieties and will further assist in the wheat breeding program.

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