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Agriculture
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Prospects and Challenges of Rice Breeding under Climate Change
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Prospects and Challenges of Rice Breeding under Climate Change

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Genotype Evaluation and Breeding".

Deadline for manuscript submissions: closed (25 September 2023) | Viewed by 9576

Special Issue Editors

Dr. Weixun Wu

E-Mail Website
Guest Editor
China National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
Interests: rice; heading date; photoperiod sensitivity; quantitative trait locus; map-based cloning; functional analysis
Special Issues, Collections and Topics in MDPI journals
Dr. Yingxin Zhang

E-Mail Website
Guest Editor
China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
Interests: rice; yield; quantitative trait locus
Special Issues, Collections and Topics in MDPI journals
Dr. Qunen Liu

E-Mail Website
Guest Editor
China National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
Interests: rice; disease resistance; gene cloning
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rice production is greatly affected by climate change. Under the background of climate change, rice breeding is facing great challenges. Firstly, increases in temperature are affecting rice cultivation with the northward expansion in Asia, and secondly, high-temperature stress is leading to a decrease in the rice heading date, and the high temperature at the heading stage may also lead to an increase in blighted grain and reduction in yield. Low-temperature stress at the transplanting stage of early rice and booting stage of late rice will also reduce rice yield. The frequent occurrence of disastrous weather requires us to cultivate new rice varieties that are resistant to high temperature, low temperature, lodging, flooding, pre-harvest sprouting, salinity, drought, disease, and insects.

This Special Issue focuses on the exploration of new rice germplasms, new genes, and new breeding techniques to resist adverse climatic conditions. This issue on the “Prospects and Challenges of Rice Breeding under Climate Change” will cover interdisciplinary research in agronomy, crop genetics and breeding, and molecular biology. All types of articles, such as original research, opinions, and reviews, are welcome.

Dr. Weixun Wu
Dr. Yingxin Zhang
Dr. Qunen Liu
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agriculture is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • high-temperature resistance
  • low-temperature resistance
  • lodging resistance
  • flooding resistance
  • ear germination resistance
  • salt and alkali resistance
  • drought resistance
  • disease resistance
  • insect resistance

Published Papers (5 papers)

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Research

12 pages, 2124 KiB  
Article
Multi-Year QTL Mapping and RNA-seq Reveal Candidate Genes for Early Floret-Opening Time in Japonica Rice
by Xiaozhou Hu, Guoliang Chen, Rui Zhang, Mengxuan Xu, Ling Zhao, Hailong Tang, Jinlong Ni and Ming Zhou
Agriculture 2023, 13(4), 859; https://doi.org/10.3390/agriculture13040859 - 13 Apr 2023
Viewed by 1495
Abstract
Floret-opening time (FOT) refers to the time between florets opening and closing within a day, and is a crucial agricultural trait for reproductive development, thermal tolerance and hybrid breeding in rice. However, little is known about the genetic basis and genes controlling FOT [...] Read more.
Floret-opening time (FOT) refers to the time between florets opening and closing within a day, and is a crucial agricultural trait for reproductive development, thermal tolerance and hybrid breeding in rice. However, little is known about the genetic basis and genes controlling FOT in rice. Here, we report the genetic mapping and transcriptome analysis of FOT in the japonica rice cultivar G23. Combining the QTLseqr and GradedPool-seq (GPS) methods, we located a major quantitative trait locus (QTL), qFOT6, on chromosome 6 in multiple years and under different environments. Integrating RNA-seq analysis, we selected 13 potential candidate genes in the qFOT6 interval that might be associated with FOT in G23. Taken together, our work uncovers a major QTL and potential candidate genes for FOT in rice, thus providing invaluable clues for rice breeding. Full article
(This article belongs to the Special Issue Prospects and Challenges of Rice Breeding under Climate Change)
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14 pages, 4200 KiB  
Article
Genetic Dissection of Tiller Number qTN4 in Rice
by Hongmei Chen, Yongyi Fan, Dian Li, Zhihao Sun, Zheyan Ruan, Huali Yang, Yiwei Kang, Weixun Wu, Qunen Liu, Xiaodeng Zhan, Liyong Cao, Ming Zhou, Shihua Cheng and Yingxin Zhang
Agriculture 2023, 13(2), 411; https://doi.org/10.3390/agriculture13020411 - 9 Feb 2023
Cited by 1 | Viewed by 1285
Abstract
Tiller number (TN) is an important trait that contributes to yield in rice (Oryza sativa L.). A set of 76 chromosome segment substitution lines (CSSLs) derived from the super-hybrid cross between Zhonghui 9308 (ZH9308) and Xieqingzao B (XQZB) was used to map [...] Read more.
Tiller number (TN) is an important trait that contributes to yield in rice (Oryza sativa L.). A set of 76 chromosome segment substitution lines (CSSLs) derived from the super-hybrid cross between Zhonghui 9308 (ZH9308) and Xieqingzao B (XQZB) was used to map quantitative trait loci (QTL) controlling tiller number (TN). A total of four QTLs were detected in Fuyang, Zhejiang Province (30.15° N, 120° E). Two QTLs were detected in Lingshui, Hainan Province (18.5° N, 110° E) in our previous study. To further map the QTL on chromosome 4, namely qTN4, the line CSSL29 with a lower tiller number was selected to cross with ZH9308 to develop the secondary F2 population. In the F2:3 population, the qTN4 was validated and subsequently narrowed down to a 4.08 Mb region. What is more, combined phenotype with genotype, qTN4 was dissected into two QTLs, qTN4.1 and qTN4.2, in the F4:5 population. The qTN4.1 and qTN4.2 explained 34.31% and 32.05% of the phenotypic variance, with an additive effect of 1.47 and 1.38, respectively. Finally, the qTN4.1 and qTN4.2 were fine-mapped into a 193.55 Kb and 175.12 Kb intervals on chromosome 4, respectively. Based on genotype and phenotype, four near-isogenic lines (NILs) were selected in the mapping populations. Compared with NILCSSL29, tiller number (TN), grain setting rate, grain length (GL), the ratio of grain length to width (LWR) and grain yield per plant of NILZH9308, NIL-qTN4.1ZH9308 and NIL-qTN4.2ZH9308 were increased, and the heading date of these three lines were earlier than that of NILCSSL29. Interestingly, among the candidate genes of qTN4.1 and qTN4.2, except for LOC_Os04g23550, none of the other genes has been cloned, indicating the existence of a novel gene-controlling tiller number. These results lay a foundation for the analysis of QTL controlling tiller number in ZH9308 and provide a theoretical basis for the application of ZH9308 in super-hybrid breeding. Full article
(This article belongs to the Special Issue Prospects and Challenges of Rice Breeding under Climate Change)
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14 pages, 2595 KiB  
Article
Comparative Quality Evaluation of Physicochemical and Amylose Content Profiling in Rice Noodles from Diverse Rice Hybrids in China
by Hang Huang, Yufei Li, Jiale Zeng, Yazi Cao, Tiancheng Zhang, Guanghui Chen and Yue Wang
Agriculture 2023, 13(1), 140; https://doi.org/10.3390/agriculture13010140 - 5 Jan 2023
Cited by 2 | Viewed by 1905
Abstract
Rice noodles are one of southern people’s favorite foods in China, so it is important to find the suitable raw rice for rice noodle making. To study the effects of different rice varieties on the quality of fresh wet rice noodles and to [...] Read more.
Rice noodles are one of southern people’s favorite foods in China, so it is important to find the suitable raw rice for rice noodle making. To study the effects of different rice varieties on the quality of fresh wet rice noodles and to explore the relationship between the quality of the rice and the quality of the fresh wet rice noodles, this study to compare the 12 hybrid rice varieties as raw materials analyzed the differences in the cooking quality, texture index, and sensory score of fresh wet rice noodles using the principal component analysis, membership function, and cluster analysis. The results showed that the quality of fresh wet rice noodles prepared from different hybrid rice materials differed significantly. The fresh wet rice noodles made from Liangyou 5836 are of good quality, and they are mainly characterized by a low rate of broken noodles and spit pulp value, high rice noodle hardness, good rice noodle elasticity, strong rice noodle chewiness, and low adhesiveness. Moreover, its sensory evaluation is also better than that of other varieties. The comprehensive evaluation of 12 hybrid rice varieties by subordinate function analysis also showed that Liangyou 5836 was the best. In addition, through principal component analysis and gray analysis, it was found that 14 related indicators of rice quality and fresh wet rice noodle quality were concentrated into four categories, among which gel consistency best reflects the quality of rice and fresh wet rice noodles. Through comprehensive analysis, it was found that an amylose content of about 22% and a gel consistency of less than 40 mm can be used as core indicators to screen varieties suitable for making rice noodles. This study is of great significance for the selection of hybrid rice for both rice quality and fresh wet rice noodle quality. Full article
(This article belongs to the Special Issue Prospects and Challenges of Rice Breeding under Climate Change)
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26 pages, 9712 KiB  
Article
Pyramiding Submergence Tolerance and Three Bacterial Blight Resistance Genes in Popular Rice Variety Hasanta through Marker-Assisted Backcross Breeding
by Goutam Das, Banshidhar Pradhan, Debendranath Bastia, Sanghamitra Samantaray, Debarchana Jena, Diptibala Rout, Paduranga Bhagwan Arsode, Vineeta Singh, Arup Kumar Mukherjee, Chander Mohan and Ramlakhan Verma
Agriculture 2022, 12(11), 1815; https://doi.org/10.3390/agriculture12111815 - 31 Oct 2022
Cited by 3 | Viewed by 2142
Abstract
Flash flooding (FF) along with bacterial blight (BB) outbreak are very destructive for rice production in the rainfed shallow-lowland (RSL) ecosystem. The presence of dynamic Xoo races with varying levels of genetic diversity and virulence renders their management extremely challenging under RSL. In [...] Read more.
Flash flooding (FF) along with bacterial blight (BB) outbreak are very destructive for rice production in the rainfed shallow-lowland (RSL) ecosystem. The presence of dynamic Xoo races with varying levels of genetic diversity and virulence renders their management extremely challenging under RSL. In this context, the marker-assisted improvement of plant resistance/tolerance has been proven as one of the most promising strategies towards the development of sustainable cultivars. The present study demonstrates the marker-assisted introgression of the submergence tolerant (Sub1) and three bacterial blight resistant genes (Xa21 + xa13 + xa5) into the genetic background of Hasanta, a long duration popular rice variety in the eastern coastal region of India. The rice genotypes, Swarna Sub1 (carrying Sub1) and IRBB66 (carrying Xa21 + xa13 + Xa7 + xa5 + Xa4) had maximum genetic similarity (0.84 and 0.73, respectively) with Hasanta; recurrent parent (RP) was used as donor. The forward analysis of target genes in F1s, IC1F1s and backcross (BC) generations was performed by linked/genic markers (Sub1bc2; pTA248, xa13prom and RM122), whereas background recovery of RP in each BC and segregating generations was performed utilizing 108 hypervariable SSR markers. Intervened speed breeding (SB) strategy and intensive phenotyping could lead the development of near isogenic lines (NILs) as to the RP in all basic traits. The performance of the near isogenic lines (NILs, BC2F3 and BC2F4), HS 232-411-391-756-37, HS 232-411-391-809-8, HS 232-411-391-756-18, HS 110-224-197-10-36, HS 232-411-391-809-81, HS 110-224-197-10-41 and HS 232-411-391-809-63 establishes the utility of marker-assisted backcross-breeding (MAB) and SB in accelerated trait introgression. The introgressed lines carrying Sub1 + Xa21 + xa13 + xa5 showed 76% to 91% survival under 14 days of submergence and durable BB resistance (percent disease index-PDI of 2.68 ± 0.26 to 6.22 ± 1.08 and lesion length, LL of 1.29 ± 0.12 to 4.2 ± 0.64 cm). Physiological analysis revealed that improved NILs, carrying Sub1 gene conquered adaptive physiological modulations, had reduced the consumption of soluble sugar and the degradation of total chlorophyll contents (TCC), and an enhanced level of Alcohol Dehydrogenase activity (ADH) and proline accumulation in all submergence regimes. The pyramided lines attained complete product profile of RP, that will contribute to sustainable rice production under RSL, particularly in the coastal region that has substantial acreage under the variety Hasanta. Full article
(This article belongs to the Special Issue Prospects and Challenges of Rice Breeding under Climate Change)
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16 pages, 2545 KiB  
Article
Fine Mapping and Candidate-Gene Analysis of an open glume multi-pistil 3 (mp3) in Rice (Oryza sativa L.)
by Yongshu Liang, Junyi Gong, Yuxin Yan, Tingshen Peng, Jinyu Xiao, Shuang Wang, Wenbin Nan, Xiaojian Qin and Hanma Zhang
Agriculture 2022, 12(10), 1731; https://doi.org/10.3390/agriculture12101731 - 20 Oct 2022
Cited by 1 | Viewed by 1760
Abstract
The rice mutant mp3 was derived from an indica–japonica cross between Rejing35 and XieqingzaoB, producing an inconstant number of pistils ranging from one to four pistils in a floret at heading stage, which also developed an open-glume with one or two seeds and [...] Read more.
The rice mutant mp3 was derived from an indica–japonica cross between Rejing35 and XieqingzaoB, producing an inconstant number of pistils ranging from one to four pistils in a floret at heading stage, which also developed an open-glume with one or two seeds and twin seedlings at mature and seedling stage. Several altered characteristics, including filling grain panicle–1 (62.90), grain-setting rate (60.48%) and grain yield plant–1 (13.42 g), decreased but an increase in 1000-grain weight (36.87 g) was observed. Genetic analysis revealed that the mp3 mutant phenotype was controlled by a single recessive gene. Using a chromosome walking strategy in the F2 population of 02428/mp3, the mp3 gene was fine mapped between L3-135 and RM7576, with a physical distance of 30.617 kb on rice chromosome 3. Four candidate genes were found in this region referred to the rice genome annotations. LOC_Os03g11614/OsMADS1 corresponded with the mutant mp3 phenotype. Sequencing showed no sequence alterations in the coding and promoter sequence of the LOC_Os03g11614/OsMADS1 of mp3. The mp3 gene may be an allelic gene with three previously reported genes but controlled different mutant floral organ phenotypes in rice. Therefore, this mp3 gene provided a novel perspective on the biological function of OsMADS1 in the development of rice floral organ. Full article
(This article belongs to the Special Issue Prospects and Challenges of Rice Breeding under Climate Change)
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