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Variations in chlorophyll content, stomatal conductance and photosynthesis in Setaria EMS mutants
TANG Chan-juan, LUO Ming-zhao, ZHANG Shuo, JIA Guan-qing, TANG Sha, JIA Yan-chao, ZHI Hui, DIAO Xian-min
2023, 22 (6): 1618-1630.   DOI: 10.1016/j.jia.2022.10.014
Abstract298)      PDF in ScienceDirect      

Chlorophyll (Chl) content, especially Chl b content, and stomatal conductance (Gs) are key factors that greatly affect net photosynthetic rate (Pn).  Setaria italica, a diploid C4 panicoid species with a simple genome and high transformation efficiency, has been widely accepted as a model in photosynthesis and drought-tolerance research.  In the current study, Chl content, Gs, and Pn of 48 Setaria mutants induced by ethyl methanesulfonate were characterized.  A total of 24, 34 and 35 mutants had significant variations in Chl content, Gs, and Pn, respectively. Correlation analysis showed that positive correlation exists between increased Gs and increased Pn, and a weak correlation between decreased Chl b content and decreased Pn was also found. Remarkably, two mutants behaved significantly decreased Chl b content but increased Pn when compared that of Yugu 1. Seven mutants behaved significantly decreased Gs but non-decreasing Pn when compared that of Yugu 1.  The current study thus identified various genetic lines, further exploration of which would be beneficial to elucidate the relationship between Chl content, Gs and Pn and the mechanism underlying why C4 species are efficient at photosynthesis and water saving.

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Identification of blast-resistance loci through genome-wide association analysis in foxtail millet (Setaria italica (L.) Beauv.)
LI Zhi-jiang, JIA Guan-qing, LI Xiang-yu, LI Yi-chu, ZHI Hui, TANG Sha, MA Jin-feng, ZHANG Shuo, LI Yan-dong, SHANG Zhong-lin, DIAO Xian-min
2021, 20 (8): 2056-2064.   DOI: 10.1016/S2095-3119(20)63196-3
Abstract198)      PDF in ScienceDirect      
Blast disease caused by the fungus Magnaporthe grisea results in significant yield losses of cereal crops across the world.  To date, very few regulatory genes contributing to blast resistance in grass species have been identified and the genetic basis of blast resistance in cereals remains elusive.  Here, a core collection of foxtail millet (Setaria italica) containing 888 accessions was evaluated through inoculation with the blast strain HN-1 and a genome-wide association study (GWAS) was performed to detect regulators responsible for blast disease resistance in foxtail millet.  The phenotypic variation of foxtail millet accessions inoculated with the blast strain HN-1 indicated that less than 1.60% of the samples were highly resistant, 35.25% were moderately resistant, 57.09% were moderately susceptible, and 6.08% were highly susceptible.  The geographical pattern of blast-resistant samples revealed that a high proportion of resistant accessions were located in lower latitude regions where the foxtail millet growing season has higher rain precipitation.  Using 720 000 SNP markers covering the Setaria genome, GWAS showed that two genomic loci from chromosomes 2 and 9 were significantly associated with blast disease resistance in foxtail millet.  Finally, eight putative genes were identified using rice blast-related transcriptomic data.  The results of this work lay a foundation for the foxtail millet blast resistance biology and provide guidance for breeding practices in this promising crop species and other cereals.
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Mapping quantitative trait loci associated with starch paste viscosity attributes by using double haploid populations of rice (Oryza sativa L.)
Tahmina SHAR, SHENG Zhong-hua, Umed ALI, Sajid FIAZ, WEI Xiang-jin, XIE Li-hong, JIAO Gui-ai, Fahad ALI, SHAO Gao-neng, HU Shi-kai, HU Pei-song, TANG Shao-qing
2020, 19 (7): 1691-1703.   DOI: 10.1016/S2095-3119(19)62726-7
Abstract127)      PDF in ScienceDirect      
The paste viscosity attributes of starch, measured by rapid visco analyzer (RVA), are important factors for the evaluation of the cooking and eating qualities of rice in breeding programs.  To determine the genetic roots of the paste viscosity attributes of rice grains, quantitative trait loci (QTLs) associated with the paste viscosity attributes were mapped, using a double haploid (DH) population derived from Zhongjiazao 17 (YK17), a super rice variety, crossed with D50, a tropic japonica variety.  Fifty-four QTLs, for seven parameters of the RVA profiles, were identified in three planting seasons.  The 54 QTLs were located on all of the 12 chromosomes, with a single QTL explaining 5.99 to 47.11% of phenotypic variation.  From the QTLs identified, four were repeatedly detected under three environmental conditions and the other four QTLs were repeated under two environments.  Most of the QTLs detected for peak viscosity (PKV), trough viscosity (TV), cool paste viscosity (CPV), breakdown viscosity (BDV), setback viscosity (SBV), and peak time (PeT) were located in the interval of RM6775–RM3805 under all three environmental conditions, with the exception of pasting temperature (PaT).  For digenic interactions, eight QTLs with six traits were identified for additive×environment interactions in all three planting environments.  The epistatic interactions were estimated only for PKV, SBV and PaT.  The present study will facilitate further understanding of the genetic architecture of eating and cooking quality (ECQ) in the rice quality improvement program.
 
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Identification of QTLs associated with cadmium concentration in rice grains
HU Da-wei, SHENG Zhong-hua, LI Qian-long, CHEN Wei, WEI Xiang-jin, XIE Li-hong, JIAO Gui-ai, SHAO Gao-neng, WANG Jian-long, TANG Shao-qing, HU Pei-song
2018, 17 (07): 1563-1573.   DOI: 10.1016/S2095-3119(17)61847-1
Abstract517)      PDF in ScienceDirect      
Cadmium (Cd) contamination in rice has been a hot topic of research because of its potential risk to human health.  In this study, a double haploid (DH) population derived from Zhongjiazao 17 (YK17) (an early-season indica cultivar)×D50 (a tropical japonica cultivar) was used to identify quantitative trait loci (QTLs) associated with Cd concentration in brown rice (CCBR) and Cd concentration in milled rice (CCMR).  Continuous and wide variation for CCBR and CCMR were observed among the DH population.  Correlation analysis revealed a positive and highly significant correlation between the two traits.  A total of 18 QTLs for CCBR and 14 QTLs for CCMR were identified in five different pot and field trials.  Two pairs of QTLs for CCBR (qCCBR2-1 and qCCBR2-2, qCCBR9-1 and qCCBR9-2) and one pair of QTLs for CCMR (qCCMR5-1 and qCCMR5-2) were detected in multiple trials.  The alleles increasing CCBR at the qCCBR2-1/qCCBR2-2 and qCCBR9-1/qCCBR9-2 QTLs were contributed by YK17 and D50, respectively, whereas the D50 allele at the qCCMR5-1/qCCMR5-2 QTLs increased CCMR.  Eight pairs of QTLs for CCBR and CCMR, qCCBR2-2 and qCCMR2-2, qCCBR3 and qCCMR3, qCCBR4-2 and qCCMR4-1, qCCBR4-3 and qCCMR4-2, qCCBR4-4 and qCCMR4-3, qCCBR5 and qCCMR5-2, qCCBR7 and qCCMR7, and qCCBR11-1 and qCCMR11-2, co-localized on chromosomes 2, 3, 4, 5, 7, and 11, respectively.  For all of these QTL pairs, except qCCBR5/qCCMR5-2, the additive effects came from YK17.  In addition, four CCMR QTLs showing significant additive×environment interaction and two pairs of CCMR QTLs with bi-allelic epistatic interactions were identified.  The results of this study could facilitate marker-assisted selection of breeding rice varieties with low Cd accumulation in grain.
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Initial detection of the quorum sensing autoinducer activity in the rumen of goats in vivo and in vitro
RAN Tao, ZHOU Chuan-she, XU Li-wei, GENG Mei-mei, TAN Zhi-liang, TANG Shao-xun, WANG Min, HAN Xue-feng, KANG Jin-he
2016, 15 (10): 2343-2352.   DOI: 10.1016/S2095-3119(16)61417-X
Abstract1726)      PDF in ScienceDirect      
    Quorum sensing (QS) is a type of microbe-microbe communication system that is widespread among the microbial world, particularly among microorganisms that are symbiotic with plants and animals. Thereby, the cell-cell signalling is likely to occur in an anaerobic rumen environment, which is a complex microbial ecosystem. In this study, using six ruminally fistulated Liuyang black goats as experimental animals, we aimed to detect the activity of quorum sensing autoinducers (AI) both in vivo and in vitro and to clone the luxS gene that encoded autoinducer-2 (AI-2) synthase of microbial samples that were collected from the rumen of goats. Neutral detergent fiber (NDF) and soluble starch were the two types of substrates that were used for in vitro fermentation. The fermented fluid samples were collected at 0, 2, 4, 6, 8, 12, 24, 36, and 48 h of incubation. The acyl-homoserine lactones (AHLs) activity was determined using gas chromatography-mass spectrometer (GC-MS) analysis. However, none of the rumen fluid extracts that were collected from the goat rumen showed the same or similar fragmentation pattern to AHLs standards. Meanwhile, the AI-2 activity, assayed using a Vibrio harveyi BB170 bioassay, was negative in all samples that were collected from the goat rumen and from in vitro fermentation fluids. Our results indicated that the activities of AHLs and AI-2 were not detected in the ruminal contents from six goats and in ruminal fluids obtained from in vitro fermentation at different sampling time-points. However, the homologues of luxS in Prevotella ruminicola were cloned from in vivo and in vitro ruminal fluids. We concluded that AHLs and AI-2 could not be detected in in vivo and in vitro ruminal fluids of goats using the current detection techniques under current dietary conditions. However, the microbes that inhabited the goat rumen had the potential ability to secrete AI-2 signaling molecules and to communicate with each other via AI-2-mediated QS because of the presence of luxS.
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