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Waxy allele diversity in waxy maize landraces of Yunnan Province, China
WU Xiao-yang, LONG Wen-jie, CHEN Dan, ZHOU Guo-yan, DU Juan, WU Shao-yun, CAI Qing
2022, 21 (2): 578-585.   DOI: 10.1016/S2095-3119(20)63471-2
Abstract286)      PDF in ScienceDirect      
Waxy maize is one of the main fresh-eating maize types, and a mutation of the waxy gene causes the waxy character of maize grains.  China is rich in waxy maize landraces, and Yunnan and its surrounding areas, are the place of origin and genetic diversity center of Chinese waxy maize.  The six known waxy alleles of Chinese waxy maize are wx-D7, wx-D10, wx-Cin4, wx-124, wx-Reina, and wx-Xuanwei.  The mutation sites of these alleles all occur in the coding region of the waxy gene, however, the mechanism by which the waxy characteristic is caused by the mutation in the regulatory region has only been reported rarely in maize.  In this study, 405 waxy maize landraces from Yunnan were used as materials to identify the insertion and deletion of a large sequence fragment in the upstream ~3.5 kb regulatory region of the waxy gene by molecular marker detection.  Three different waxy alleles were identifed in this study: wx-PIF/Harbinger, wx-hAT and wxElote2.  These three types of mutations all represented transposons inserted into the regulatory region of the waxy gene.  Wx-PIF/Harbinger was a 304-bp MITE class transposon insertion belonging to the PIF/Harbinger family, while wx-hAT was a 560-bp MITE class transposon insertion belonging to the hAT family, and wx-Elote2 was a 6 560-bp LTR-like transposon insertion.  In this study, the alleles were identifed for more than 70% of the waxy maize landraces in Yunnan, which provids a basis for the utilization of these waxy maize landraces.
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Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding
REN Yun, CHEN Dan, LI Wen-jie, TAO Luo, YUAN Guo-qiang, CAO Ye, LI Xue-mei, DENG Qi-ming, WANG Shi-quan, ZHENG Ai-ping, ZHU Jun, LIU Huai-nian, WANG Ling-xia, LI Ping, LI Shuang-cheng
2021, 20 (1): 35-45.   DOI: 10.1016/S2095-3119(20)63256-7
Abstract226)      PDF in ScienceDirect      
Hybrid rice significantly contributes to the food supply worldwide.  Backbone parents play important roles in elite hybrid rice breeding systems.  In this study, we performed pedigree-based analysis of the elite backbone parent rice variety, namely, Shuhui 527 (SH527, Oryza sativa), to exploit key genome regions during breeding.  Twenty-four cultivars (including SH527, its six progenitors and 17 derived cultivars) were collected and analyzed with high-density single nucleotide polymorphism (SNP) array.  Scanning all these cultivars with genome-wide SNP data indicated the unique contributions of progenitors to the SH527 genome and identified the key genomic regions of SH527 conserved within all its derivatives.  These findings were further supported by known rice yield-related genes or unknown QTLs identified by genome-wide association study.  This study reveals several key regions for SH527 and provides insights into hybrid rice breeding.
 
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Novel and favorable genomic regions for spike related traits in a wheat germplasm Pubing 3504 with high grain number per spike under varying environments
CHEN Dan, WU Xiao-yang, WU Kuo, ZHANG Jin-peng, LIU Wei-hua, YANG Xin-ming, LI Xiu-quan, LU Yu-qing, LI Li-hui
2017, 16 (11): 2386-2401.   DOI: 10.1016/S2095-3119(17)61711-8
Abstract607)      PDF in ScienceDirect      
   Grain number per spike (GNPS) is a major factor in wheat yield breeding.  A new wheat germplasm Pubing 3504 shows superior features in spike traits.  To elucidate the genetic basis of spike and yield related traits in Pubing 3504, 282 F2:3 families were generated from the cross Pubing 3504×Jing 4839, and seven spike and yield related traits, including GNPS, spike length (SL), kernel number per spikelet (KPS), spikelet number per spike (SNS), thousand-grain weight (TGW), spike number per plant (SNP), and plant height (HT) were investigated.  Correlation analysis indicated significant positive correlations between GNPS and spike-related traits, including KPS, SNS, and SL, especially KPS.  A genetic map was constructed using 190 polymorphic simple sequence repeat (SSR), expressed sequence tag (EST)-SSR, and sequence-tagged-site (STS) markers.  For the seven traits measured, a total of 37 quantitative trait loci (QTLs) in a single-environment analysis and 25 QTLs in a joint-environment analysis were detected.  Additive effects of 70.3% (in a single environment) and 57.6% (in a joint environment) of the QTLs were positively contributed by Pubing 3504 alleles.  Five important genomic regions on chromosomes 1A, 4A, 4B, 2D, and 4D could be stably detected in different environments.  Among these regions, the marker interval Xmag834–Xbarc83 on the short arm of chromosome 1A was a novel important genomic region that included QTLs controlling GNPS, KPS, SNS, TGW, and SNP with stable environmental repeatability.  This genomic region can improve the spike trait and may play a key role in improving wheat yield in the future.  We deduced that this genomic region was vital to the high GNPS of Pubing 3504.
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Gene and protein expression profiling analysis of young spike development in large spike wheat germplasms
CHEN Dan, ZHANG Jin-peng, LIU Wei-hua, WU Xiao-yang, YANG Xin-ming, LI Xiu-quan, LU Yu-qing, LI Li-hui
2016, 15 (4): 744-754.   DOI: 10.1016/S2095-3119(15)61179-0
Abstract1705)      PDF in ScienceDirect      
The wheat grain number per spike (GNPS) is a major yield-limiting factor in wheat-breeding programs. Germplasms with a high GNPS are therefore valuable for increasing wheat yield potential. To investigate the molecular characteristics of young spike development in large-spike wheat germplasms with high GNPS, we performed gene and protein expression profiling analysis with three high-GNPS wheat lines (Pubing 3228, Pubing 3504 and 4844-12) and one low-GNPS control variety (Fukuho). The phenotypic data for the spikes in two growth seasons showed that the GNPS of the three large-spike wheat lines were significantly higher than that of the Fukuho control line. The Affymetrix wheat chip and isobaric tags for relative and absolute quantitation-tandam mass spectrometry (iTRAQ-MS/MS) technology were employed for gene and protein expression profiling analyses of young spike development, respectively, at the floret primordia differentiation stage. A total of 598 differentially expressed transcripts (270 up-regulated and 328 down-regulated) and 280 proteins (122 up- regulated and 158 down-regulated) were identified in the three high-GNPS lines compared with the control line. We found that the expression of some floral development-related genes, including Wknox1b, the AP2 domain protein kinase and the transcription factor HUA2, were up-regulated in the high-GNPS lines. The expression of the SHEPHERD (SHD) gene was up-regulated at both the transcript and protein levels. Overall, these results suggest that multiple regulatory pathways, including the CLAVATA pathway and the meristem-maintaining KNOX protein pathway, take part in the development of the high-GNPS phenotype in our wheat germplasms.
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Energy requirements of Dorper×thin-tailed Han crossbred ewes during non-pregnancy and lactation
LOU Can, SI Bing-wen, DENG Kai-dong, MA Tao, JIANG Cheng-gang, TU Yan, ZHANG Nai-feng, JI Shou-kun, CHEN Dan-dan, DIAO Qi-yu
2015, 14 (12): 2605-2617.   DOI: 10.1016/S2095-3119(14)60963-1
Abstract1453)      PDF in ScienceDirect      
This experiment was conducted to investigate the energy requirement of Dorper×thin-tailed Han crossbred ewes during non-pregnancy and lactation. Fifteen ewes after parturition were randomly assigned to three treatments: ad libitum (100%) feed intake and 80 or 60% ad libitum intake, and another nine non-pregnant ewes were assigned to a blank control group. Digestibility trials were performed in the non-pregnant ewes and in the lactating ewes on the 20th, 50th, and 80th d of lactation. In parallel with the digestibility trial, a respirometry experiment was conducted to determine the methane and carbon dioxide production with an open-circuit respirometry system that was equipped with respiratory chambers. The net energy (NE) and metabolizable energy (ME) requirements for maintenance and growth were calculated using the carbon and nitrogen balance method. The results revealed that the carbon (C) and nitrogen (N) excretions and energy losses at faeces and urine, as well as the output of methane and CO2, increased significantly with decreasing feed intake (P<0.01). The apparent digestibilities of C in the stages of non-pregnancy and early, middle and late lactation were 55.8–58.3%, 62.5–73.8%, 64.8– 71.3%, and 61.7–65.0%, respectively, and the apparent digestibilities of N were 45.2–51.3%, 73.7–82.7%, 72.8–80.5%, and 73.6–76.5%, respectively. The corresponding energy apparent digestibilities were 52.0–56.3%, 60.7–76.6%, 61.0–68.8%, and 61.4–67.7%, respectively. The ME/DE (digestible energy) values were 79.5–85.9%, 79.4–83.5%, 81.0%–85.3% and 78.6–82.9%, respectively. The maintenance requirements of NE, ME, and the efficiencies of ME utilisation for maintenance during the stages of non-pregnancy and early, middle and late lactation were 215.5, 253.1, 247.7, and 244.7 kJ kg–1 BW0.75 d, and 372.4, 327.1, 320.9, and 362.0 kJ kg–1 BW0.75 d, and 0.58, 0.77, 0.77, and 0.68, respectively. The ME requirement for the growth of non-pregnant ewes was 31.3 MJ kg–1 BW gain.
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Inheritance and Availability of High Grain Number Per Spike in Two Wheat Germplasm Lines
CHEN Dan, ZHANG Jin-peng, WANG Jian-sheng, YANG Xin-ming, LIU Wei-hua, GAO Ai-nong, LI
2012, 12 (9): 1409-1416.   DOI: 10.1016/S1671-2927(00)8673
Abstract1535)      PDF in ScienceDirect      
Grain number per spike (GNPS) is a major factor in wheat yield breeding. The development of high GNPS germplasm is widely emphasized in wheat-yield breeding. This paper reported two high GNPS wheat germplasm lines, Pubing 3228 and Pubing 3504, which had a stable and wide adaptability to different ecological regions. By exploring a nested cross design with reciprocals using Pubing 3228 or Pubing 3504 as a common parent and investigating the GNPS phenotypes of F1 hybrids in 2007-2008 and F2 populations in 2008-2009 of different cross combinations, the narrow-sense GNPS heritability was up to 49.58 and 52.23%, respectively. Genetic model analysis predictions suggested that GNPS in Pubing 3228 and Pubing 3504 was mainly controlled by additive genetic effects. Correlation analysis results between GNPS and 1 000- kernel weight (TKW) of F2 populations showed that TKW was not influenced with the increase of GNPS. The good coordination among three yield components of spike number per plant (SNPP), GNPS, and TKW in the F2 segregating population implied that selection of good candidate individuals in breeding programs would be relatively straightforward. Overall, our results indicated that Pubing 3228 and Pubing 3504 are two potential germplasm lines for yield improvement of GNPS in pedigree selection of wheat breeding.
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