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Association mapping of lignin response to Verticillium wilt through an eight-way MAGIC population in Upland cotton
TIAN Xiao-min, HAN Peng, WANG Jing, SHAO Pan-xia, AN Qiu-shuang, Nurimanguli AINI, YANG Qing-yong, YOU Chun-yuan, LIN Hai-rong, ZHU Long-fu, PAN Zhen-yuan, NIE Xin-hui
2023, 22 (5): 1324-1337.   DOI: 10.1016/j.jia.2022.08.034
Abstract398)      PDF in ScienceDirect      

Lignin metabolism plays a pivotal role in plant defense against pathogens and is always positively correlated as a response to pathogen infection.  Thus, understanding resistance genes against pathogens in plants depends on a genetic analysis of lignin response.  In the study, eight upland cotton lines were used to construct a multi-parent advanced generation intercross (MAGIC) population (n=280), which exhibited peculiar characteristics from the convergence of various alleles coding for advantageous traits.  To measure the lignin response to Verticillium wilt (LRVW), artificial disease nursery (ADN) and rotation nursery (RN) were prepared for MAGIC population planting in four environments.  The stem lignin contents were collected, and the LRVW was measured with the lignin value of ADN/RN in each environment, which showed great variation.  A total of 9323 high-quality single-nucleotide polymorphism (SNP) markers obtained from the Cotton-SNP63K array were employed for genotyping the MAGIC population.  The SNPs were distributed through the whole genome with 4.78 SNP/Mb density, ranging from 1.14 (ChrA06) to 10.08 (ChrD08).  A genome-wide association study was performed using a mixed linear model (MLM) for LRVW, and three stable quantitative trait loci (QTLs), qLRVW-A04, qLRVW-A10 and qLRVW-D05, were identified in more than two environments.  Two key candidate genes, Ghi_D05G01046 and Ghi_D05G01221, were selected within the QTLs through the combination of variations in the coding sequence, induced expression patterns, and function annotations, both of which presented nonsynonymous mutations in coding regions and were strongly induced by Verticillium dahliae. Ghi_D05G01046 encodes a leucine-rich extensin (LRx) protein, which is involved in Arabidopsis cell wall biosynthesis and organization.  Ghi_D05G01221 encodes a transcriptional co-repressor novel interactor of jaz (NINJA), which functions in the jasmonic acid (JA) signaling pathway.  In summary, the study creates valuable genetic resources for breeding and QTL mapping and opens up a new perspective to uncover the genetic basis of VW resistance in upland cotton.

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Effects of planting patterns on yield, quality, and defoliation in machine-harvested cotton
WANG Fang-yong, HAN Huan-yong, LIN Hai, CHEN Bing, KONG Xian-hui, NING Xin-zhu, WANG Xu-wen, YU Yu, LIU Jing-de
2019, 18 (9): 2019-2028.   DOI: 10.1016/S2095-3119(19)62604-3
Abstract122)      PDF in ScienceDirect      
The aim of this study was to elucidate the effects of different machine-harvested cotton-planting patterns on defoliation, yield, and fiber quality in cotton and to provide support for improving the quality of machine-harvested cotton.  In the 2015 and 2016 growing seasons, the Xinluzao 45 (XLZ45) and Xinluzao 62 (XLZ62) cultivars, which are primarily cultivated in northern Xinjiang, were used as study materials.  Conventional wide-narrow row (WNR), wide and ultra-narrow row (UNR), wide-row spacing with high density (HWR), and wide-row spacing with low density (LWR) planting patterns were used to assess the effects of planting patterns on defoliation, yield, and fiber quality.  Compared with WNR, the seed cotton yields were significantly decreased by 2.06–5.48% for UNR and by 2.50–6.99% for LWR, respectively.  The main cause of reduced yield was a reduction in bolls per unit area.  The variation in HWR yield was –1.07–1.07% with reduced bolls per unit area and increased boll weight, thus demonstrating stable production.  In terms of fiber quality indicators, the planting patterns only showed significant effects on the micronaire value, with wide-row spacing patterns showing an increase in the micronaire values.  The defoliation and boll-opening results showed that the number of leaves and dried leaves in HWR was the lowest among the four planting patterns.  Prior to the application of defoliating agent and before machine-harvesting, the numbers of leaves per individual plant in HWR were decreased by 14.45 and 25.00% on average, respectively, compared with WNR, while the number of leaves per unit area was decreased by 27.44 and 36.21% on average, respectively.  The rates of boll-opening and defoliation in HWR were the highest.  Specifically, the boll-opening rate before defoliation and machine-harvesting in HWR was 44.54 and 5.94% higher on average than in WNR, while the defoliation rate prior to machine-harvesting was 3.45% higher on average than in WNR.  The numbers of ineffective defoliated leaves and leaf trash in HWR were the lowest, decreased by 33.40 and 32.43%, respectively, compared with WNR.  In conclusion, the HWR planting pattern is associated with a high and stable yield, does not affect fiber quality, promotes early maturation, and can effectively decrease the amount of leaf trash in machine-picked seed cotton, and thus its use is able to improve the quality of machine-harvested cotton.
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Genome-Wide Expression Profile of Maize Root Response to Phosphorus Deficiency Revealed by Deep Sequencing
SU Shun-zhong, WU Ling, LIU Dan, LU Yan-li, LIN Hai-jian, ZHANG Shu-zhi, SHEN Ya-ou, LIU Hai-lan, ZHANG Zhi-ming, RONG Ting-zhao, ZHANG Xiao, TIAN Yue-hui, NIE Zhi , GAO Shi-bin
2014, 13 (6): 1216-1229.   DOI: 10.1016/S2095-3119(13)60614-0
Abstract2058)      PDF in ScienceDirect      
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.
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