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Genetic diversity and association mapping for salinity tolerance in Bangladeshi rice landraces

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The Crop Journal 2015年第5期3卷 440-444页

作者： Reza M.Emon Mirza M.Islam Jyotirmoy Halder Yeyang Fan Chinese National center for rice Improvement/State Key Laboratory of rice Biology China National Rice Research Institute Bangladesh Institute of Nuclear Agriculture

Breeding for salinity tolerance using Bangladeshi rice landraces and understand genetic diversity has been limited by the complex and polygenic nature of salt tolerance in rice genotypes. A genetic diversity and association mapping analysis was conducted using 96 germplasm accessions with variable response to salt stress at the seedling stage. These included86 landraces and 10 indica varieties and lines including Nona Bokra, from southern Bangladesh. A total of 220 alleles were detected at 58 Simple Sequence Repeat(SSR) marker loci randomly distributed on all 12 rice chromosomes and 8 Sequence Tagged Site(STS) markers developed for genes SKC1, DST, and SalT. The average gene diversity was 0.5075 and polymorphism information content value was 0.4426, respectively. Cluster analysis revealed that 68 and 21 accessions were clustered into 2 distinct groups, possibly corresponding to indica and japonica groups, respectively and the remaining 7 landraces were classified as an admixed group. In addition to Wn11463, the STS marker for SKC1, RM22418 on Chr. 8 was significantly associated with salinity tolerance, at the location of a QTL detected in previous studies. Our findings of favorable alleles associated with salinity tolerance in Bangladeshi rice landraces, as well as the development of STS markers for salt tolerance genes, will be helpful in future efforts to breed salinity tolerance in rice.

关键词： Oryza sativa L Salinity tolerance Seedling stage S

Validation of qGSIO, a quantitative trait locus for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.)

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Journal of Integrative Agriculture 2017年第1期16卷 16-26页

作者： WANG Zhen CHEN Jun-yu ZHU Yu-jun FAN Ye-yang ZHUANG Jie-yun State Key Laboratory of rice Biology and Chinese National center for rice Improvement China National Rice Research Institute Hangzhou 310006 P.R. China

Grain size is a major determinant of grain weight and a trait having important impact on grain quality in rice. The objective of this study is to detect QTLs for grain size in rice and identify important QTLs that have not been well characterized before. The QTL mapping was first performed using three recombinant inbred line populations derived from indica rice crosses Teqing/IRBB lines, Zhenshan 97/Milyang 46, Xieqingzao/Milyang 46. Fourteen QTLs for grain length and 10 QTLs for grain width were detected, including seven shared by two populations and 17 found in one population. Three of the seven com- mon QTLs were found to coincide in position with those that have been cloned and the four others remained to be clarified. One of them, qGSIO located in the interval RM6100-RM228 on the long arm of chromosome 10, was validated using F2：3 populations and near isogenic lines derived from residual heterozygotes for the interval RM6100-RM228. The QTL was found to have a considerable effect on grain size and grain weight, and a small effect on grain number. This region was also previously detected for quality traits in rice in a number of studies, providing a good candidate for functional analysis and breeding utilization.

关键词： grain size quantitative trait locus residual heterozygote rice (Oryza sativa L.)

Alternate phenotype–genotype selection for developing superior high-yielding irrigated rice lines

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The Crop Journal 2018年第2期6卷 191-201页

作者： Yonnelle Dea Moukoumbi Raafat El-Namaky Koffi Djaman Daouda Mbodj Baboucarr Manneh Irrigated rice Breeding Unit Africa Rice Center(Africa Rice)Sahel Regional StationBP 96 Saint LouisSenegal National Institute of Agricultural research Gros bouquetPMB 16169LibrevilleGabon rice research&Training center(RRTC) 33717 Sakha Kafr SheikhEgypt

Increase grain yield potential is one of the most important objectives of any cereal crop breeding program. To efficiently develop superior rice lines by the introgression of favorable alleles for yield and yield component traits, a strategy of alternate phenotype–genotype selection was used. The present study aimed to(i) investigate the allelic diversity of loci associated with major yield-component traits and(ii) phenotype and genotype advanced populations derived from crosses between NERICA-L-20 and Giza178 for yield component traits using agro-morphological descriptors and GRi SP polymorphic markers to select superior high-yielding rice lines. A total of 100 F2:3 progeny were selected from 1000 F2 plants and genotyped with 16 polymorphic markers linked to four major yield-component traits. Four promising F2:3 lines(ARS 563–14, ARS 563–62, ARS 563–286, and ARS 563–41)bearing combinations of desirable alleles were selected. A selected set of 20 F2:4 lines showed moderate to high heritability for all target traits. Fourteen F2:5 lines derived from ARS 563–14 and 17 F2:5 from ARS 563–286 families were evaluated in preliminary trials to estimate yield gain. The three top lines, ARS 563–286–16-1-1, ARS 563–286–5-1-1, and ARS563–14–10-1-1, showed an increase of more than 10% grain yield over the best check, Sahel108, which is widely cultivated in the Senegal River valley. The 16 markers linked to the target yield component traits can be used to fast-track breeding programs targeting rice productivity.

关键词： Marker rice Pedigree selection Yield

Genetic dissection of a thousand-grain weight quantitative trait locus on rice chromosome 1

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Chinese Science Bulletin 2008年第15期53卷 2326-2332页

作者： YU ShouWu YANG ChangDeng FAN YeYang ZHUANG JieYun LI XiMing State Key Laboratory of rice Science Chinese National Center for Rice Improvement China National Rice Research InstituteHangzhou 310006 China

Thousand-grain weight (TGWT) is an important factor affecting grain yield as well as grain quality in rice. A quantitative trait locus (QTL) qTGWT1-1 for TGWT was detected previously near DNA marker RG532 on the short arm of chromosome 1 in a recombinant inbred line (RIL) population derived from the indica-indica rice cross Zhengshan97B (ZS97B)/Milyang46 (MY46). In this study, two residual het-erozygous lines (RHLs), Ch1 and Ch2, derived from the ZS97B/MY46 RIL F7 population, were used to develop two F6 populations, RIL-1 and RIL-2. The genome of Ch1 and Ch2 contains a heterozygous region flanked by RM1―RM3746 and RM151―RM243 on the short arm of chromosome 1, respectively, but is homozygous in other regions. Two tightly linked QTLs, Gw1-1 and Gw1-2, with the same additive direction and similar effect on TGWT, were detected in the region of QTL qTGWT1-1 in population RIL-2. No QTL was detected in the population RIL-1. Four individual RHLs from the population RIL-2 carrying heterozygous segments flanked by RM151―RM10404, RM10381―RM243, RM10435―RM259 and RM10398―RM5359, respectively, were chosen to develop four F2 populations. Ten maternal homozy-gotes and 10 paternal homozygotes were selected from each of the four F2 populations derived from the four RHLs. The four sets of near isogenic lines (NILs) were grown for phenotyping of TGWT and delimitation of Gw1-1 and Gw1-2. Results showed that Gw1-1 and Gw1-2 were located in the intervals RM10376―RM10398 and RM10404―RM1344 which cover 392.9 and 308.5 kb regions, respectively. The enhancing alleles were from ZS97B at both loci, and no significant interactions were detected. Genetic dissection of Gw1-1 and Gw1-2 has laid a foundation for their cloning and molecular breeding of grain yield and quality in rice.

关键词：水稻遗传基因染色体线粒体 QTL

Effect of Biochar on Relieving Cadmium Stress and Reducing Accumulation in Super japonica rice

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Journal of Integrative Agriculture 2014年第3期13卷 547-553页

作者： ZHANG Zhen-yu MENG Jun DANG Shu CHEN Wen-fu Liaoning Biochar Engineering & Technology research center Key Laboratory of rice Biology and Breeding Ministry of Agriculture/Key Laboratory of Northern Japonica Super Rice Breeding Ministry of Education/Rice Research Institute Shenyang Agricultural University

It is of great importance to solve the threats induced by cadmium pollution on crops. This paper examined the effect of biochar on cadmium accumulation in japonica rice and revealed the mechanism underlying the response of protective enzyme system to cadmium stress. Biochar derived from rice straw was applied at two application rates under three cadmium concentrations. Shennong 265, super japonica rice variety, was selected as the test crop. The results indicated that cadmium content in above-ground biomass of rice increased with increasing soil cadmium concentrations, but the biochar application could suppress the accumulation of cadmium to some extent. Under high concentrations of cadmium, content of free proline and MDA （malondialdehyde） were high, so did the SOD （superoxide dismutase）, POD （peroxidase） and CAT （catalase） activity in the flag leaf of rice. However, the protective enzyme activities remained at low level when biochar was added.

关键词： super japonica rice biochar cadmium stress cadmium accumulation

Progress in super-hybrid rice breeding

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The Crop Journal 2017年第2期5卷 100-102页

作者： Longping Yuan China National Hybrid rice research and Development center Changsha 410125 China

*** To meet the food demand of the Chinese people in the 21st century,a super-rice breeding program aimed at increasing rice yield was initiated by the Ministry of Agriculture of China in *** is divided into four phases,with the following yield targets:10.5 t ha^(-1)(phase I,1996–2000),12 t ha^(-1)(phase II,2001–2005),13.5 t ha^(-1)(phase III,2006–2015),and 15 t ha^(-1)(phase IV,2016–2020)~[1].The average yield of super-rice should be verified in two locations of 6.7 ha each in two consecutive years.

关键词： inter-subspecific heterosis indica japonica morphological characteristics yield increase

NRL3 Interacts with OsK4 to Regulate Heading Date in rice

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rice science 2022年第3期29卷 237-246页

作者： CHEN Wei CAI Yicong Shakeel AHMAD WANG Yakun AN Ruihu TANG Shengjia GUO Naihui WEI Xiangjin TANG Shaoqing SHAO Gaoneng JIAO Guiai XIE Lihong HU Shikai SHENG Zhonghua HU Peisong Key Laboratory of Crop Physiology Ecology and Genetic BreedingMinistry of Education/Collaboration Center for Double-Season Rice Modernization ProductionJiangxi Agricultural University/Research Center of Super Rice Engineering and TechnologyJiangxi ProvinceNanchang 330045China State Key Laboratory of rice Biology/Key Laboratory of rice Biology and Breeding Ministry of Agriculture and Rural Affairs/China National Rice Improvement Center/China National Rice Research InstituteHangzhou 310006China

NRL3 is essential for the growth and development of rice *** this study,we found that the loss function of NRL3 also delayed heading date under natural long daylight and short daylight *** yeast two-hybrid and the bimolecular fluorescence complementation proved that NRL3interacts with OsK4,a Snf1-related ***4 localized to the nucleus and expressed in various rice *** rhythmic expression pattern of Os K4 was similar to NRL3 under long daylight and short daylight ***-out mutants of Os K4 exhibited early heading under long daylight conditions,indicating that it acts as a negative regulator of heading date in ***,the OsK4 mutant under the nrl3 mutant background rescued the late heading phenotype of nrl3 under long daylight conditions,suggesting that Os K4 functions downstream of ***,both NRL3 and Os K4 controlled heading date through regulating the expression of Hd3a and RFT1 *** findings shed light on the heading date regulation in rice and provide a sound theoretical base to improve regional adaptability of rice.

关键词： Oryza sativa heading date NRL3 gene OsK4 gene negative regulator loss function

Molecular identification of the cytoplasmic male sterile source from Dongxiang wild rice(Oryza rufipogon Griff.)

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Journal of Integrative Agriculture 2017年第8期16卷 1669-1675页

作者： YAN Song ZHU Shan MAO Ling-hua HUANG Ren-liang XIONG Hong-liang SHEN Lin-jun SHEN Xian-hua rice National Engineering Laboratory(Nanchang)/Nanchang Sub-center National Rice Improvement Center/Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics/Rice Research InstituteJiangxi Academy of Agricultural Sciences Key Laboratory of Crop Physiology Ecology and Genetic BreedingMinistry of Education/College of AgronomyJiangxi Agricultural University Jiangxi Super-rice research and Development center Jiangxi Academy of Agricultural Sciences

The use of cytoplasm male sterility （CMS） is crucial for three-line hybrid seed production. Two types of CMS have been discovered from Dongxiang wild rice, namely the wild abortion type CMS （CMS-WA） and the Dongxiang wild type CMS （CMS-DW）. In this study, we show the molecular identification of the two types of CMS in Dongxiang wild rice. WA352, which conferred CMS-WA, was not detected in Dongxiang wild iice, implying Dongxiang wild rice does not carry the CMS- WA source. Further analysis of WA352 in DYIA, a CMS-DW line, by PCR amplification and sequencing, revealed two insertion-deletion polymorphisms occurred in CMS-DW compared to WA352 of CMS-WA. It was reported that WA352 was comprised of an unknown origin sequence and partial sequences of three open reading frames （ORFs）, orf284, orf224 and orf288. The 42-bp insertion was located between the two segments of orf224 and orf288, which created a new chimeric ORF, orf216. This new ORF was also detected in CMS-HL. Based on the 9-bp deletion in orf284, a specific mitochon- drial marker of DW-M1 was developed, which could be used to specifically distinguish the DW-type source. Moreover, semi-quantitative RT-PCR analysis preliminarily suggested that both orf216 and orf284 could be considered as candidates for CMS-DW. These findings present a preliminary understanding of CMS-DW at the molecular level.

关键词： Dongxiang wild rice cytoplasm male sterile WA352 orf216 orf284 mitochondrial marker

Oriented Generation of Novel Thermo-Sensitive Genic Male Sterile Lines with Improved Grain Shape and Outcrossing Rate in Early-Season rice

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rice science 2024年第2期31卷 129-133,I0001-I0016页

作者： ZHANG Huali CHEN Junyu LI Ruiqing WANG Huimei DAI Dongqing LIANG Minmin WU Mingyue MA Liangyong State Key Laboratory of rice Biology and Breeding/Chinese National center for rice Improvement China National Rice Research InstituteHangzhou 310006China

Two-line hybrid rice with excellent quality is preferred in the Chinese ***,there is a trade-off between reducing costs for hybrid seed production and lowering the outcrossing rate of the sterile line,which is largely determined by the stigma exsertion rate(SER).In this study,we constructed mutants of male sterility lines with improved grain length(GL)and SER in three elite early-season indica rice varieties through targeted manipulation of the TMS5 and GS3 genes using CRISPR/Cas9-mediated multiplex *** obtained a series of marker-free gs3 single mutants and gs3tms5 double mutants with significantly higher SER,longer grains,and increased 1000-grain weight compared with the wild type(WT).Importantly,the typically thermo-sensitive genic male sterile(TGMS)trait with a higher SER was observed in gs3tms5 mutants,and their F1 hybrids exhibited remarkable improvements in grain shape and yield-related *** findings provided an efficient method to generate new valuable TGMS germplasm with improved SER through the mutagenesis of GS3 and TMS5 synergistically,and demonstrated that GS3 had pleiotropic effects on grain size,SER,and grain quality in early-season indica rice.

关键词： sterile elite season