@article{bekele_methane_2024,
	title = {Methane production from locally available ruminant feedstuffs in {Ethiopia} – {An} \textit{in vitro} study},
	volume = {312},
	issn = {0377-8401},
	url = {https://www.sciencedirect.com/science/article/pii/S0377840124001056},
	doi = {10.1016/j.anifeedsci.2024.115977},
	abstract = {Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P{\textless}0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6\%; indigenous plants 3.1–16.9\%; crop residues 15.8–20.6\%; agro-industrial by-products 12.8–18.7\%), and within category, e.g., Trifolium acaule (3.1\%), Acacia nilotica L. (7.1\%), Ziziphus spina-christi (9.9\%), brewer’s spent grains (BSG) (12.8\%), local liquor (areki) residues (14.1\%), and local beer (tella) residues (15.1\%). A negative relationship was observed between CT content and in vitro CH4 yield, with a stronger (P{\textless}0.05) correlation for soluble CTs (R2 = 0.46) than cell-bound CTs (R2 = 0.25) and total CTs (R2 = 0.29). Based on methanogenic properties and effects of CTs on in vitro CH4 yield, indigenous plants should be prioritized in ruminant rations in Ethiopia. Making nutritional composition and CH4 data publicly available could help develop environmentally sound, cost-effective rations for ruminant livestock, benefiting local farmers and leading to more sustainable and efficient livestock production in Ethiopia.},
	urldate = {2024-05-06},
	journal = {Animal Feed Science and Technology},
	author = {Bekele, Wondimagegne and Huhtanen, Pekka and Zegeye, Abiy and Simachew, Addis and Siddique, Abu Bakar and Albrectsen, Benedicte Riber and Ramin, Mohammad},
	month = jun,
	year = {2024},
	keywords = {CH, CH gas percentage, Local feeds, condensed tannins, dry matter digestibility},
	pages = {115977},
}

Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P\textless0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6%; indigenous plants 3.1–16.9%; crop residues 15.8–20.6%; agro-industrial by-products 12.8–18.7%), and within category, e.g., Trifolium acaule (3.1%), Acacia nilotica L. (7.1%), Ziziphus spina-christi (9.9%), brewer’s spent grains (BSG) (12.8%), local liquor (areki) residues (14.1%), and local beer (tella) residues (15.1%). A negative relationship was observed between CT content and in vitro CH4 yield, with a stronger (P\textless0.05) correlation for soluble CTs (R2 = 0.46) than cell-bound CTs (R2 = 0.25) and total CTs (R2 = 0.29). Based on methanogenic properties and effects of CTs on in vitro CH4 yield, indigenous plants should be prioritized in ruminant rations in Ethiopia. Making nutritional composition and CH4 data publicly available could help develop environmentally sound, cost-effective rations for ruminant livestock, benefiting local farmers and leading to more sustainable and efficient livestock production in Ethiopia.

@article{shi_high-quality_2024,
	title = {High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar},
	volume = {195},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae078},
	doi = {10.1093/plphys/kiae078},
	abstract = {Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77\% accuracy on the training set and 74\% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.},
	number = {1},
	urldate = {2024-05-03},
	journal = {Plant Physiology},
	author = {Shi, Tian-Le and Jia, Kai-Hua and Bao, Yu-Tao and Nie, Shuai and Tian, Xue-Chan and Yan, Xue-Mei and Chen, Zhao-Yang and Li, Zhi-Chao and Zhao, Shi-Wei and Ma, Hai-Yao and Zhao, Ye and Li, Xiang and Zhang, Ren-Gang and Guo, Jing and Zhao, Wei and El-Kassaby, Yousry Aly and Müller, Niels and Van de Peer, Yves and Wang, Xiao-Ru and Street, Nathaniel Robert and Porth, Ilga and An, Xinmin and Mao, Jian-Feng},
	month = may,
	year = {2024},
	pages = {652--670},
}

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

@article{hasan_redox_2024,
	title = {Redox signalling in plant–nematode interactions: {Insights} into molecular crosstalk and defense mechanisms},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	shorttitle = {Redox signalling in plant–nematode interactions},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14925},
	doi = {10.1111/pce.14925},
	abstract = {Plant–parasitic nematodes, specifically cyst nematodes (CNs) and root-knot nematodes (RKNs), pose significant threats to global agriculture, leading to substantial crop losses. Both CNs and RKNs induce permanent feeding sites in the root of their host plants, which then serve as their only source of nutrients throughout their lifecycle. Plants deploy reactive oxygen species (ROS) as a primary defense mechanism against nematode invasion. Notably, both CNs and RKNs have evolved sophisticated strategies to manipulate the host's redox environment to their advantage, with each employing distinct tactics to combat ROS. In this review, we have focused on the role of ROS and its scavenging network in interactions between host plants and CNs and RKNs. Overall, this review emphasizes the complex interplay between plant defense mechanism, redox signalling and nematode survival tactics, suggesting potential avenues for developing innovative nematode management strategies in agriculture.},
	language = {en},
	urldate = {2024-05-03},
	journal = {Plant, Cell \& Environment},
	author = {Hasan, M. Shamim and Lin, Ching-Jung and Marhavy, Peter and Kyndt, Tina and Siddique, Shahid},
	month = apr,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14925},
	keywords = {ROS, antioxidants, cyst nematodes, effectors, root-knot nematodes},
}

Plant–parasitic nematodes, specifically cyst nematodes (CNs) and root-knot nematodes (RKNs), pose significant threats to global agriculture, leading to substantial crop losses. Both CNs and RKNs induce permanent feeding sites in the root of their host plants, which then serve as their only source of nutrients throughout their lifecycle. Plants deploy reactive oxygen species (ROS) as a primary defense mechanism against nematode invasion. Notably, both CNs and RKNs have evolved sophisticated strategies to manipulate the host's redox environment to their advantage, with each employing distinct tactics to combat ROS. In this review, we have focused on the role of ROS and its scavenging network in interactions between host plants and CNs and RKNs. Overall, this review emphasizes the complex interplay between plant defense mechanism, redox signalling and nematode survival tactics, suggesting potential avenues for developing innovative nematode management strategies in agriculture.

@article{wang_slnac3_2024,
	title = {{SlNAC3} suppresses cold tolerance in tomatoes by enhancing ethylene biosynthesis},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14933},
	doi = {10.1111/pce.14933},
	abstract = {Low temperature stress poses a significant challenge to the productivity of horticultural crops. The dynamic expression of cold-responsive genes plays a crucial role in plant cold tolerance. While NAC transcription factors have been extensively studied in plant growth and development, their involvement in regulating plant cold tolerance remains poorly understood. In this study, we focused on the identification and characterisation of SlNAC3 as the most rapid and robust responsive gene in tomato under low temperature conditions. Manipulating SlNAC3 through overexpression or silencing resulted in reduced or enhanced cold tolerance, respectively. Surprisingly, we discovered a negative correlation between the expression of CBF and cold tolerance in the SlNAC3 transgenic lines. These findings suggest that SlNAC3 regulates tomato cold tolerance likely through a CBF-independent pathway. Furthermore, we conducted additional investigations to identify the molecular mechanisms underlying SINAC3-mediated cold tolerance in tomatoes. Our results revealed that SlNAC3 controls the transcription of ethylene biosynthetic genes, thereby bursting ethylene release in response to cold stress. Indeed, the silencing of these genes led to an augmentation in cold tolerance. This discovery provides valuable insights into the regulatory pathways involved in ethylene-mediated cold tolerance in tomatoes, offering potential strategies for developing innovative approaches to enhance cold stress resilience in this economically important crop species.},
	language = {en},
	urldate = {2024-05-03},
	journal = {Plant, Cell \& Environment},
	author = {Wang, Tao and Ma, Xuemin and Chen, Ying and Wang, Cuicui and Xia, Zhenxiao and Liu, Zixi and Gao, Lihong and Zhang, Wenna},
	month = may,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14933},
	keywords = {NAC transcription factor, cold response},
}

Low temperature stress poses a significant challenge to the productivity of horticultural crops. The dynamic expression of cold-responsive genes plays a crucial role in plant cold tolerance. While NAC transcription factors have been extensively studied in plant growth and development, their involvement in regulating plant cold tolerance remains poorly understood. In this study, we focused on the identification and characterisation of SlNAC3 as the most rapid and robust responsive gene in tomato under low temperature conditions. Manipulating SlNAC3 through overexpression or silencing resulted in reduced or enhanced cold tolerance, respectively. Surprisingly, we discovered a negative correlation between the expression of CBF and cold tolerance in the SlNAC3 transgenic lines. These findings suggest that SlNAC3 regulates tomato cold tolerance likely through a CBF-independent pathway. Furthermore, we conducted additional investigations to identify the molecular mechanisms underlying SINAC3-mediated cold tolerance in tomatoes. Our results revealed that SlNAC3 controls the transcription of ethylene biosynthetic genes, thereby bursting ethylene release in response to cold stress. Indeed, the silencing of these genes led to an augmentation in cold tolerance. This discovery provides valuable insights into the regulatory pathways involved in ethylene-mediated cold tolerance in tomatoes, offering potential strategies for developing innovative approaches to enhance cold stress resilience in this economically important crop species.

@article{mishra_adventitious_2024,
	title = {Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials},
	volume = {15},
	issn = {1664-462X},
	shorttitle = {Adventitious rooting in response to long-term cold},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1352830/full},
	doi = {10.3389/fpls.2024.1352830},
	abstract = {{\textless}p{\textgreater}Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial {\textless}italic{\textgreater}Arabis alpina{\textless}/italic{\textgreater} to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in {\textless}italic{\textgreater}A. alpina{\textless}/italic{\textgreater} stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of {\textless}italic{\textgreater}DR5{\textless}/italic{\textgreater} auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2024-05-03},
	journal = {Frontiers in Plant Science},
	author = {Mishra, Priyanka and Roggen, Adrian and Ljung, Karin and Albani, Maria C. and Vayssières, Alice},
	month = apr,
	year = {2024},
	note = {Publisher: Frontiers},
	keywords = {Adventitious root, Arabis alpina, Clonal propagation, Transcriptome, alpine, extended cold exposure, phytohormones},
}

\textlessp\textgreaterArctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial \textlessitalic\textgreaterArabis alpina\textless/italic\textgreater to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in \textlessitalic\textgreaterA. alpina\textless/italic\textgreater stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of \textlessitalic\textgreaterDR5\textless/italic\textgreater auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.\textless/p\textgreater