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Mabreja AD, Reyes VP, Soe TK, Shimakawa K, Makihara D, Nishiuchi S, Doi K. Evaluation of Grain-Filling-Related Traits Using Taichung 65 x DV85 Chromosome Segment Substitution Lines (TD-CSSLs) of Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:289. [PMID: 38256843 PMCID: PMC10818708 DOI: 10.3390/plants13020289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024]
Abstract
Grain yield of rice consists of sink capacity and grain filling. There are some genes known to contribute to sink capacity, but few genes associated with grain filling are known. We conducted a genetic analysis on yield-related traits by using a chromosome segment substitution line population that have introgression from DV85, an aus variety of rice, in the background of T65, a japonica variety. Refined whole-genome genotypes of the 43 TD-CSSLs were obtained by genotyping-by-sequencing. The effects of previously detected quantitative trait loci (QTLs), qNSC1 and qNSC2, were confirmed by the amount of non-structural carbohydrate (NSC) at 5 days after heading (DAH). The CSSL for qSWTR11, the QTL for decrease in shoot weight during the maturity stage, showed the highest NSC at 5 DAH and lowest at 35 DAH. The brown rice yield of these lines were not stably significant. Most of the sink-related traits correlated between the 2 tested years, but most of the grain-filling traits did not show correlation between the 2 years. Correlation analysis revealed that the sink capacity is stable and primarily determines the yield, and grain filling is more affected by the environment. In addition, biomass production before heading and during the maturity stage contributes to higher yield in TD-CSSLs, and the amount of translocation of stem reserve does not affect much to the yield. We conclude that higher NSC at the heading stage and rapid decrease in shoot biomass during the maturity stage did not directly contribute to the yield formation in the japonica genetic background.
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Affiliation(s)
- Abebaw Dessie Mabreja
- Graduate School of Bioagicultural Science, Nagoya University, Chikusa, Nagoya 464-8601, Aichi, Japan; (A.D.M.); (V.P.R.); (K.S.); (S.N.)
- Ethiopian Institute of Agricultural Research, Fogera National Rice Research and Training Center, Bahir Dar 1937, Ethiopia
| | - Vincent Pamugas Reyes
- Graduate School of Bioagicultural Science, Nagoya University, Chikusa, Nagoya 464-8601, Aichi, Japan; (A.D.M.); (V.P.R.); (K.S.); (S.N.)
| | - Than Kutay Soe
- Graduate School of Bioagicultural Science, Nagoya University, Chikusa, Nagoya 464-8601, Aichi, Japan; (A.D.M.); (V.P.R.); (K.S.); (S.N.)
| | - Kodai Shimakawa
- Graduate School of Bioagicultural Science, Nagoya University, Chikusa, Nagoya 464-8601, Aichi, Japan; (A.D.M.); (V.P.R.); (K.S.); (S.N.)
| | - Daigo Makihara
- International Center for Research and Education in Agriculture, Nagoya University, Chikusa, Nagoya 464-8601, Aichi, Japan;
| | - Shunsaku Nishiuchi
- Graduate School of Bioagicultural Science, Nagoya University, Chikusa, Nagoya 464-8601, Aichi, Japan; (A.D.M.); (V.P.R.); (K.S.); (S.N.)
| | - Kazuyuki Doi
- Graduate School of Bioagicultural Science, Nagoya University, Chikusa, Nagoya 464-8601, Aichi, Japan; (A.D.M.); (V.P.R.); (K.S.); (S.N.)
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Tomita R, Reyes VP, Fukuta Y, Gichuhi EW, Kikuta M, Menge DM, Doi K, Makihara D. Genetic Variation of Blast ( Pyricularia oryzae Cavara) Resistance in the Longistaminata Chromosome Segment Introgression Lines (LCSILs) and Potential for Breeding Use in Kenya. PLANTS (BASEL, SWITZERLAND) 2023; 12:863. [PMID: 36840212 PMCID: PMC9966461 DOI: 10.3390/plants12040863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/01/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
In Kenya's rice-growing areas, Basmati varieties have been produced in monoculture since the late 1980s. This has resulted in the breakdown of the resistance (R) gene-mediated response of the local Basmati varieties to blast disease caused by Pyricularia oryzae. To improve blast resistance in Kenyan Basmati varieties, continuous identification of R genes and suitable breeding materials for Basmati are necessary. Longistaminata chromosome segment introgression lines (LCSILs) with the Kernel Basmati genetic background, developed using a rice line called potential low-input adaptable-1 (pLIA-1) derived from a cross between Taichung 65 (T65) (a rice variety in the Japonica Group) and O. longistaminata, are expected to contain useful blast R genes derived from O. longistaminata or T65. In this study, we investigated the genetic variation of blast R genes in LCSILs and their parents by using a new international differential system for designating blast races based on the gene-for-gene theory and molecular characterization using single nucleotide polymorphism (SNP) markers. LCSILs and their parents were classified into three groups-A, B1, and B2-based on reaction patterns to the standard differential blast isolates (SDBIs). Group A, including pLIA-1, showed the highest resistance in all groups, followed by groups B1 and B2. Kernel Basmati in group B1 was considered to possess Pik-p or Pi7(t), Pi19(t), and other unknown R genes. In addition to these R genes, LCSIL 6, 12, 27, 28, and 40, in group A, were determined to possess one of Pish, Piz-t, or both genes that confer resistance to the Kenyan blast races. These lines can be used for efficiently pyramiding blast R genes in the local Basmati varieties.
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Affiliation(s)
- Rena Tomita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Vincent Pamugas Reyes
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshimichi Fukuta
- Japan International Research Center for Agricultural Sciences, Tsukuba 305-8686, Japan
| | - Emily Waringa Gichuhi
- Kenya Agricultural and Livestock Research Organization, Kerugoya P.O. Box 298-10300, Kenya
| | - Mayumi Kikuta
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Daniel Makori Menge
- Kenya Agricultural and Livestock Research Organization, Kerugoya P.O. Box 298-10300, Kenya
| | - Kazuyuki Doi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Daigo Makihara
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya 464-8601, Japan
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Goto I, Neang S, Kuroki R, Reyes VP, Doi K, Skoulding NS, Taniguchi M, Yamauchi A, Mitsuya S. QTL analysis for sodium removal ability in rice leaf sheaths under salinity using an IR-44595/318 F 2 population. FRONTIERS IN PLANT SCIENCE 2022; 13:1002605. [PMID: 36304401 PMCID: PMC9592983 DOI: 10.3389/fpls.2022.1002605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Over-accumulation of salt in rice plants is an effect of salt stress which decreases growth and grain yield. Salt removal ability in leaf sheaths is a tolerance mechanism to decrease salt entry and accumulation in leaf blades and maintain photosynthesis under salinity. In this study, a QTL analysis of removal ability of sodium ions (Na+) in leaf sheaths and Na+ accumulation-related traits, was conducted using F2 population between two rice varieties, IR-44595 with superior Na+ removal ability, and 318 with contrasting Na+ removal ability in leaf sheaths under salinity. Suggestive QTLs for Na+ removal ability in leaf sheaths were found on chromosomes 4 and 11. The suggestive QTL on chromosome 11 overlapped with other significant QTLs for Na+ concentration in shoots, leaf blades and leaf sheaths, and Na+/K+ ratio in leaf blades. Correlation analysis indicated that Na+ removal ability in leaf sheaths is important in reducing Na+ accumulation in leaf blades. The varietal difference of Na+ removal ability in leaf sheaths at the whole plant level was greater at lower NaCl concentrations and became smaller as the treatment NaCl concentration increased. Although the Na+ removal ability in leaf sheath was comparable between IR-44595 and 318 under high salinity at the whole plant level, the younger leaves of IR-44595 still showed a higher Na+ sheath-blade ratio than 318, which implied the Na+ removal ability functions in the younger leaves in IR-44595 to reduce Na+ entry in young leaf blades even under high salinity.
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Affiliation(s)
- Itsuki Goto
- Laboratory of Plant Physiology and Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Sarin Neang
- Laboratory of Crop Stress Regulation, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Ministory of Agriculture, Forestry and Fishery, Phnom Penh, Cambodia
| | - Ryuichi Kuroki
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Vincent Pamugas Reyes
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kazuyuki Doi
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Mitsutaka Taniguchi
- Laboratory of Plant Physiology and Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Akira Yamauchi
- Laboratory of Crop Stress Regulation, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shiro Mitsuya
- Laboratory of Plant Physiology and Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Laboratory of Crop Stress Regulation, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Fu L, Wu J, Yang S, Jin Y, Liu J, Yang M, Rasheed A, Zhang Y, Xia X, Jing R, He Z, Xiao Y. Genome-wide association analysis of stem water-soluble carbohydrate content in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2897-2914. [PMID: 32594265 DOI: 10.1007/s00122-020-03640-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/19/2020] [Indexed: 05/14/2023]
Abstract
GWAS identified 36 potentially new loci for wheat stem water-soluble carbohydrate (WSC) contents and 13 pleiotropic loci affecting WSC and thousand-kernel weight. Five KASP markers were developed and validated. Water-soluble carbohydrates (WSC) reserved in stems contribute significantly to grain yield (GY) in wheat. However, knowledge of the genetic architecture underlying stem WSC content (SWSCC) is limited. In the present study, 166 diverse wheat accessions from the Yellow and Huai Valleys Winter Wheat Zone of China and five other countries were grown in four well-watered environments. SWSCC at 10 days post-anthesis (10DPA), 20DPA and 30DPA, referred as WSC10, WSC20 and WSC30, respectively, and thousand-kernel weight (TKW) were assessed. Correlation analysis showed that TKW was significantly and positively correlated with WSC10 and WSC20. Genome-wide association study was performed on SWSCC and TKW with 373,106 markers from the wheat 660 K and 90 K SNP arrays. Totally, 62 stable loci were detected for SWSCC, with 36, 24 and 19 loci for WSC10, WSC20 and WSC30, respectively; among these, 36 are potentially new, 16 affected SWSCC at two or three time-points, and 13 showed pleiotropic effects on both SWSCC and TKW. Linear regression showed clear cumulative effects of favorable alleles for increasing SWSCC and TKW. Genetic gain analyses indicated that pyramiding favorable alleles of SWSCC had simultaneously improved TKW. Kompetitive allele-specific PCR markers for five pleiotropic loci associated with both SWSCC and TKW were developed and validated. This study provided a genome-wide landscape of the genetic architecture of SWSCC, gave a perspective for understanding the relationship between WSC and GY and explored the theoretical basis for co-improvement of WSC and GY. It also provided valuable loci and markers for future breeding.
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Affiliation(s)
- Luping Fu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jingchun Wu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Shurong Yang
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730000, Gansu, China
| | - Yirong Jin
- Dezhou Institute of Agricultural Sciences, Dezhou, 253000, Shandong, China
| | - Jindong Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, 518000, China
| | - Mengjiao Yang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Ruilian Jing
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing, 100081, China.
| | - Yonggui Xiao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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