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Article ; Online: Transcriptome and metabolome profiling of unheading in F1 hybrid rice

Jie WANG / Shao-bo WEI / Chun-chao WANG / Najeeb Ullah KHAN / Zhan-ying ZHANG / Wensheng WANG / Xiu-qin ZHAO / Hong-liang ZHANG / Zi-chao LI / Yong-ming GAO

Journal of Integrative Agriculture, Vol 19, Iss 10, Pp 2367-

2020 Volume 2382

Abstract: Heading date is a crucial agronomic trait. However, rice usually delays heading due to the photoperiod, temperature, hormones or age. The present research was conducted to analyze the mechanism controlling heading date in F1 hybrid rice. We constructed ... ...

Abstract	Heading date is a crucial agronomic trait. However, rice usually delays heading due to the photoperiod, temperature, hormones or age. The present research was conducted to analyze the mechanism controlling heading date in F1 hybrid rice. We constructed two test-crossing populations using two introgression lines (ILs), P20 and P21 coming from SH527/FH838 as the male parent, respectively, and male sterile line Jin23A as the female parent. Meanwhile, the F1 hybrids of H20, obtained by mating P20 with Jin23A and having no heading, and H21, from the crossing between P21 and Jin23A having normal heading, were both observed under long days. Here, we analyzed the photoperiodic response of F1 hybrids by transcriptome and metabolome profiling. The greater differences displayed in the transcriptome and the metabolome were caused by photoperiod (exogenous) instead of genes (endogenous). The coping mechanism resulted from long days (LD) in H20, leading to differences in the circadian rhythm and glutathione metabolism relative to other samples. The circadian oscillator and GSH/GSSG cycle typically regulate ROS homeostasis, and both of them are responsible for modulating ROS in H20 under LD condition. Both circadian rhythm genes and the reported genes related to heading date function via the DHD1/OsMFT1-Ehd1-RFT1-OsMADS14/OsMADS18 pathway and the glutathione metabolism pathway by regulating oxidative reduction processes. Both pathways are involved in the heading process and they interacted through the oxidative reduction process which was induced by photoperiod regulation, and all of them collectively modulated the heading process. The results of this study will be helpful for unraveling the mechanism of F1 hybrid responses to unheading under LD condition.
Keywords	F1 hybrid rice ; unheading ; transcriptome profiles ; metabolome profiles ; Agriculture (General) ; S1-972
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: QTL mapping of grain appearance quality traits and grain weight using a recombinant inbred population in rice (Oryza sativa L.)

GAO, Fang-yuan / Guang-jun REN / Juan-sheng REN / Li-hua ZENG / Ling QIU / Xiang-wen SU / Xian-jun LU / Xian-ting WU / Yong-ming GAO

Chinese Academy of Agricultural Sciences Journal of integrative agriculture. 2016 Aug., v. 15, no. 8

2016

Abstract: Grain appearance quality traits, measured as grain length (GL), grain width (GW), length to width ratio (LWR), grain thickness (GT) and the percentage of grain with chalkiness (PGWC), as well as 1 000-grain weight (TGW), are very important factors that ... ...

Abstract	Grain appearance quality traits, measured as grain length (GL), grain width (GW), length to width ratio (LWR), grain thickness (GT) and the percentage of grain with chalkiness (PGWC), as well as 1 000-grain weight (TGW), are very important factors that contribute to rice grain quality and yield. To detect quantitative trait loci (QTLs) affecting these traits, we developed a set of recombinant inbred lines (RILs) derived from Gang46B (G46B) and K1075, a G46B introgression line with lower PGWC. Based on a linkage map containing 33 simple sequence repeat (SSR) markers, a total of 15 additive QTLs governing six measured traits were identified on 4 chromosomes across two environments. Of these, the five major QTLs which controlled GW, LWR, GT, PGWC, and TGW, each explaining up to 44.30, 55.29, 62.30, 30.94, and 28.78% of the variation, respectively, were found in the same interval of RM18004–RM18068 on chromosome 5. The G46B alleles contributed to the increase in GW, GT and PGWC at all loci, as well as the increase in TGW at its major QTL locus. Significant interactions between additive QTL and the environment were found at most loci, in which the largest, accounting for 15.06% of variation, was observed between qPGWC-5 and the environment. A total of 15 epistasis QTLs were detected for all the traits, and GL, GW and PGWC had significant epistasis QTLs based on environment interactions with minor effects. These results are valuable for future map-based cloning of the QTLs and the collaborative improvement of G46B in grain appearance quality and yield.
Keywords	alleles ; chromosome mapping ; epistasis ; grain quality ; inbred lines ; introgression ; loci ; microsatellite repeats ; molecular cloning ; Oryza sativa ; quantitative trait loci ; rice
Language	English
Dates of publication	2016-08
Size	p. 1693-1702.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2660426-7
ISSN	2095-3119
ISSN	2095-3119
DOI	10.1016/S2095-3119(15)61259-X
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: QTL mapping of grain appearance quality traits and grain weight using a recombinant inbred population in rice (Oryza sativa L.)

Fang-yuan GAO / Li-hua ZENG / Ling QIU / Xian-jun LU / Juan-sheng REN / Xian-ting WU / Xiang-wen SU / Yong-ming GAO / Guang-jun REN

Journal of Integrative Agriculture, Vol 15, Iss 8, Pp 1693-

2016 Volume 1702

Abstract	Grain appearance quality traits, measured as grain length (GL), grain width (GW), length to width ratio (LWR), grain thickness (GT) and the percentage of grain with chalkiness (PGWC), as well as 1 000-grain weight (TGW), are very important factors that contribute to rice grain quality and yield. To detect quantitative trait loci (QTLs) affecting these traits, we developed a set of recombinant inbred lines (RILs) derived from Gang46B (G46B) and K1075, a G46B introgression line with lower PGWC. Based on a linkage map containing 33 simple sequence repeat (SSR) markers, a total of 15 additive QTLs governing six measured traits were identified on 4 chromosomes across two environments. Of these, the five major QTLs which controlled GW, LWR, GT, PGWC, and TGW, each explaining up to 44.30, 55.29, 62.30, 30.94, and 28.78% of the variation, respectively, were found in the same interval of RM18004–RM18068 on chromosome 5. The G46B alleles contributed to the increase in GW, GT and PGWC at all loci, as well as the increase in TGW at its major QTL locus. Significant interactions between additive QTL and the environment were found at most loci, in which the largest, accounting for 15.06% of variation, was observed between qPGWC-5 and the environment. A total of 15 epistasis QTLs were detected for all the traits, and GL, GW and PGWC had significant epistasis QTLs based on environment interactions with minor effects. These results are valuable for future map-based cloning of the QTLs and the collaborative improvement of G46B in grain appearance quality and yield.
Keywords	QTL ; appearance quality ; 1 000-grain weight ; recombination inbred lines (RIL) ; rice ; Agriculture (General) ; S1-972
Subject code	669
Language	English
Publishing date	2016-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Harnessing the hidden genetic diversity for improving multiple abiotic stress tolerance in rice (Oryza sativa L.).

Jauhar Ali / Jian-Long Xu / Yong-Ming Gao / Xiu-Fang Ma / Li-Jun Meng / Ying Wang / Yun-Long Pang / Yong-Sheng Guan / Mei-Rong Xu / Jastin E Revilleza / Neil J Franje / Shao-Chuan Zhou / Zhi-Kang Li

PLoS ONE, Vol 12, Iss 3, p e

2017 Volume 0172515

Abstract: To develop superior rice varieties with improved yield in most rainfed areas of Asia/Africa, we started an introgression-breeding program for simultaneously improving yield and tolerances of multiple abiotic stresses. Using eight BC1 populations derived ... ...

Abstract	To develop superior rice varieties with improved yield in most rainfed areas of Asia/Africa, we started an introgression-breeding program for simultaneously improving yield and tolerances of multiple abiotic stresses. Using eight BC1 populations derived from a widely adaptable recipient and eight donors plus three rounds of phenotypic selection, we developed 496 introgression lines (ILs) with significantly higher yield under drought, salt and/or non-stress conditions in 5 years. Six new varieties were released in the Philippines and Pakistan and many more are being evaluated in multi-location yield trials for releasing in several countries. Marker-facilitated genetic characterization revealed three interesting aspects of the breeding procedure: (1) the donor introgression pattern in specific BC populations was characteristic; (2) introgression frequency in different genomic regions varied considerably, resulting primarily from strong selection for the target traits; and (3) significantly lower heterozygosity was observed in BC progenies selected for drought and salinity tolerance. Applying strong phenotypic selection under abiotic stresses in early segregating generations has major advantages for not only improving multiple abiotic stress tolerance but also achieving quicker homozygosity in early generations. This breeding procedure can be easily adopted by small breeding programs in developing countries to develop high-yielding varieties tolerant of abiotic stresses. The large set of trait-specific ILs can be used for genetic mapping of genes/QTL that affect target and non-target traits and for efficient varietal development by designed QTL pyramiding and genomics-based recurrent selection in our Green Super Rice breeding technology.
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Genetic Dissection of Low Phosphorus Tolerance Related Traits Using Selected Introgression Lines in Rice

Chao, XIANG / Jie, REN / Xiu-qin, ZHAO / Zai-song, DING / Jing, ZHANG / Chao, WANG / Jun-wei, ZHANG / Joseph, Charles Augustino / Qiang, ZHANG / Yun-long, PANG / Yong-ming, GAO / Ying-yao, SHI

Rice science. 2015 Nov., v. 22, no. 6

2015

Abstract: To dissect the genetic basis of low phosphorus tolerance (LPT), 114 BC2F4 introgression lines (ILs) were developed from Shuhui 527 and Minghui 86 (recurrent parents), and Yetuozai (donor parent). The progenies were tested for 11 quantitative traits under ...

Abstract	To dissect the genetic basis of low phosphorus tolerance (LPT), 114 BC2F4 introgression lines (ILs) were developed from Shuhui 527 and Minghui 86 (recurrent parents), and Yetuozai (donor parent). The progenies were tested for 11 quantitative traits under three treatments including normal fertilization in normal soil (as control), normal fertilization in barren soil and low phosphorus stress in barren soil in Langfang, Hebei Province, China. Moreover, the ILs were investigated at the seedling stage using nutrient solution culture method in greenhouse in Beijing, China. A total of 49 main-effect quantitative trait loci (QTLs) underlying yield related traits were identified in Langfang, and their contributions to phenotypic variations ranged from 6.7% to 16.5%. Among them, 25 (51.0%) QTLs had favorable alleles from donor parent. A total of 48 main-effect QTLs were identified for LPT-related traits in Beijing, and their contributions to phenotypic variations ranged from 7.7% to 16.6%. Among them, 21 (43.8%) QTLs had favorable alleles from donor parent. About 79.6% of the QTLs can be detected repeatedly under two or more treatments, especially QTLs associated with spikelet number per panicle, spikelet fertility and 1000-grain weight, displaying consistent phenotypic effects. Among all the detected QTLs, eight QTLs were simultaneously identified under low phosphorus stress across two environments. These results can provide useful information for the genetic dissection of LPT in rice.
Keywords	alleles ; greenhouses ; introgression ; nutrient solutions ; panicles ; parents ; phenotype ; phenotypic variation ; phosphorus ; quantitative trait loci ; quantitative traits ; rice ; seedlings ; soil ; spikelets ; China
Language	English
Dates of publication	2015-11
Size	p. 264-274.
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1672-6308
DOI	10.1016/j.rsci.2015.05.020
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Improvement of Yield and Its Related Traits for Backbone Hybrid Rice Parent Minghui 86 Using Advanced Backcross Breeding Strategies

Hong-jun ZHANG / Hui WANG / Guo-you YE / Yi-liang QIAN / Ying-yao SHI / Jia-fa XIA / Ze-fu LI / Ling-hua ZHU / Yong-ming GAO / Zhi-kang LI

Journal of Integrative Agriculture, Vol 12, Iss 4, Pp 561-

2013 Volume 570

Abstract: How to overcome yield stagnation is a big challenge to rice breeders. An effective method for quickly developing new cultivars is to further improve an outstanding cultivar. In this study, three advanced backcross populations under yield selection that ... ...

Abstract	How to overcome yield stagnation is a big challenge to rice breeders. An effective method for quickly developing new cultivars is to further improve an outstanding cultivar. In this study, three advanced backcross populations under yield selection that consist of 123 BC2F2:4 introgression lines (ILs) were developed by crossing Minghui 86 (recurrent parent, RP) with three high-yielding varieties (donors), namely, ZDZ057, Fuhui 838, and Teqing, respectively. The progeny testing allowed the identification of 12 promising ILs that had significantly higher mean grain yields than Minghui 86 in two environments. A total of 55 QTLs that affect grain yield and its related traits were identified, which included 50 QTLs that were detected using the likelihood ratio test based on stepwise regression (RSTEP-LRT) method, and eight grain yield per plant (GY) QTLs were detected using chi-squared (c2) test. Among these QTLs, five QTLs were simultaneously detected in different populations and 22 QTLs were detected in both environments. The beneficial donor alleles for increased GY and its related traits were identified in 63.6% (35 out of 55) of the QTLs. These promising ILs and QTLs identified will provide the elite breeding materials and genetic information for further improvement of the grain yield for Minghui 86 through pyramiding breeding.
Keywords	rice (Qryza sativa L.) ; quantitative trait locus (QTL) ; selective introgression population ; yield ; Agriculture (General) ; S1-972
Subject code	669
Language	English
Publishing date	2013-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dissecting genetic networks underlying complex phenotypes

Fan Zhang / Hu-Qu Zhai / Andrew H Paterson / Jian-Long Xu / Yong-Ming Gao / Tian-Qing Zheng / Rong-Ling Wu / Bin-Ying Fu / Jauhar Ali / Zhi-Kang Li

PLoS ONE, Vol 6, Iss 1, p e

the theoretical framework.

2011 Volume 14541

Abstract: Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate ... ...

Abstract	Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many 'downstream' loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and "co-adapted" gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2011-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Improvement of Yield and Its Related Traits for Backbone Hybrid Rice Parent Minghui 86 Using Advanced Backcross Breeding Strategies

ZHANG, Hong-jun / Guo-you YE / Hui WANG / Jia-fa XIA / Ling-hua ZHU / Yi-liang QIAN / Ying-yao SHI / Yong-ming GAO / Ze-fu LI / Zhi-kang LI

Chinese Academy of Agricultural Sciences Journal of integrative agriculture. 2013 Apr., v. 12

2013

Abstract	How to overcome yield stagnation is a big challenge to rice breeders. An effective method for quickly developing new cultivars is to further improve an outstanding cultivar. In this study, three advanced backcross populations under yield selection that consist of 123 BC2F2:4 introgression lines (ILs) were developed by crossing Minghui 86 (recurrent parent, RP) with three high-yielding varieties (donors), namely, ZDZ057, Fuhui 838, and Teqing, respectively. The progeny testing allowed the identification of 12 promising ILs that had significantly higher mean grain yields than Minghui 86 in two environments. A total of 55 QTLs that affect grain yield and its related traits were identified, which included 50 QTLs that were detected using the likelihood ratio test based on stepwise regression (RSTEP-LRT) method, and eight grain yield per plant (GY) QTLs were detected using chi-squared (c2) test. Among these QTLs, five QTLs were simultaneously detected in different populations and 22 QTLs were detected in both environments. The beneficial donor alleles for increased GY and its related traits were identified in 63.6% (35 out of 55) of the QTLs. These promising ILs and QTLs identified will provide the elite breeding materials and genetic information for further improvement of the grain yield for Minghui 86 through pyramiding breeding.
Keywords	alleles ; backcrossing ; grain yield ; high-yielding varieties ; hybrids ; introgression ; new variety ; progeny testing ; quantitative trait loci
Language	English
Dates of publication	2013-04
Size	p. 561-570.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2660426-7
ISSN	2095-3119
ISSN	2095-3119
DOI	10.1016/S2095-3119(13)60273-7
Database	NAL-Catalogue (AGRICOLA)

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