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5. Current Research Trends in Biological Science Vol. 4

Author

Pringgenies, Delianis, additional, Dewi, Kartika, additional, Apriliyani, Pramita, additional, Boli, Zamblé Bi Irié Abel, additional, Camara, Fatoumata, additional, Toka, Djegba Marie, additional, Koussemon, Marina, additional, Koffi-Nevry, Rose, additional, Olufemi, Akanni E., additional, Folarin, O. R., additional, Igbeneghu, C., additional, Okuno, Kazutoshi, additional, Fukuoka, Shuichi, additional, Asuquo, Nkoyo Edet, additional, Antai, Slyvester Peter, additional, Carpentieri-Pipolo, Valeria, additional, Ravimannan, Nirmala, additional, Ynalvez, Ruby A., additional, Kinnon, Carmen Cruz-Mac, additional, Ynalvez, Marcus A., additional, Okereke, J. N., additional, Ogidi, O. I., additional, Obasi, K. O., additional, Mardones, A., additional, González, M., additional, Rivas-Mancilla, C., additional, Vega, R., additional, Augsburger, A., additional, Encina, F., additional, Ríos, P. De los, additional, Chutia, Jnandabhiram, additional, Borah, S. P., additional, Tanti, Bhaben, additional, Ire, Francis Sopuruchukwu, additional, Okoli, Augustine Onwuchekwa, additional, Berebon, Dinebari P., additional, Beeram, Eswari, additional, Washa, Washa B., additional, Merghem, Mounira, additional, and Dahamna, Saliha, additional

Published
2020
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6. MORE PANICLES 3 , a natural allele of OsTB1/FC1 , impacts rice yield in paddy fields at elevatedCO 2levels

Author

Takai, Toshiyuki, primary, Taniguchi, Yojiro, additional, Takahashi, Megumu, additional, Nagasaki, Hideki, additional, Yamamoto, Eiji, additional, Hirose, Sakiko, additional, Hara, Naho, additional, Akashi, Hiroko, additional, Ito, Jun, additional, Arai‐Sanoh, Yumiko, additional, Hori, Kiyosumi, additional, Fukuoka, Shuichi, additional, Sakai, Hidemitsu, additional, Tokida, Takeshi, additional, Usui, Yasuhiro, additional, Nakamura, Hirofumi, additional, Kawamura, Kensuke, additional, Asai, Hidetoshi, additional, Ishizaki, Takuma, additional, Maruyama, Kyonoshin, additional, Mochida, Keiichi, additional, Kobayashi, Nobuya, additional, Kondo, Motohiko, additional, Tsuji, Hiroyuki, additional, Tsujimoto, Yasuhiro, additional, Hasegawa, Toshihiro, additional, and Uga, Yusaku, additional

Published
2023
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11. MORE PANICLES 3, a natural allele of OsTB1/FC1, impacts rice yield in paddy fields at elevated CO2 levels.

Author

Takai, Toshiyuki, Taniguchi, Yojiro, Takahashi, Megumu, Nagasaki, Hideki, Yamamoto, Eiji, Hirose, Sakiko, Hara, Naho, Akashi, Hiroko, Ito, Jun, Arai‐Sanoh, Yumiko, Hori, Kiyosumi, Fukuoka, Shuichi, Sakai, Hidemitsu, Tokida, Takeshi, Usui, Yasuhiro, Nakamura, Hirofumi, Kawamura, Kensuke, Asai, Hidetoshi, Ishizaki, Takuma, and Maruyama, Kyonoshin

Subjects
RICE, ATMOSPHERIC carbon dioxide, PADDY fields, LOCUS (Genetics), ALLELES, AGRICULTURAL productivity
Abstract

SUMMARY: Improving crop yield potential through an enhanced response to rising atmospheric CO2 levels is an effective strategy for sustainable crop production in the face of climate change. Large‐sized panicles (containing many spikelets per panicle) have been a recent ideal plant architecture (IPA) for high‐yield rice breeding. However, few breeding programs have proposed an IPA under the projected climate change. Here, we demonstrate through the cloning of the rice (Oryza sativa) quantitative trait locus for MORE PANICLES 3 (MP3) that the improvement in panicle number increases grain yield at elevated atmospheric CO2 levels. MP3 is a natural allele of OsTB1/FC1, previously reported as a negative regulator of tiller bud outgrowth. The temperate japonica allele advanced the developmental process in axillary buds, moderately promoted tillering, and increased the panicle number without negative effects on the panicle size or culm thickness in a high‐yielding indica cultivar with large‐sized panicles. The MP3 allele, containing three exonic polymorphisms, was observed in most accessions in the temperate japonica subgroups but was rarely observed in the indica subgroup. No selective sweep at MP3 in either the temperate japonica or indica subgroups suggested that MP3 has not been involved and utilized in artificial selection during domestication or breeding. A free‐air CO2 enrichment experiment revealed a clear increase of grain yield associated with the temperate japonica allele at elevated atmospheric CO2 levels. Our findings show that the moderately increased panicle number combined with large‐sized panicles using MP3 could be a novel IPA and contribute to an increase in rice production under climate change with rising atmospheric CO2 levels. Significance Statement: Genetic enhancement of crop responses to the rising atmospheric CO2 levels is one way to improve crop productivity under the projected climate change. We demonstrate that a cloned rice (Oryza sativa) quantitative trait locus, MP3, promoted tillering, moderately increased the panicle number without negative effects on the panicle size or culm thickness, and clearly increased the grain yield under elevated atmospheric CO2 conditions, indicating the value for designing a novel high‐yielding ideotype under the projected climate change. [ABSTRACT FROM AUTHOR]

Published
2023
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15. Identification of chromosome regions for high-temperature tolerance in the japonica rice cultivar 'Genkitsukushi' (Oryza sativa L.).

Author

Miyahara, Katsunori, Wada, Takuya, Fukuoka, Shuichi, Miyazaki, Masayuki, Yamaguchi, Osamu, Ishibashi, Masafumi, Kondo, Motohiko, Hamaoka, Norimitsu, and Ishibashi, Yushi

Subjects
RICE, LOCUS (Genetics), CHROMOSOMES, GLOBAL warming, HIGH temperatures
Abstract

Degradation of the appearance of rice grains due to high temperatures during ripening is a serious problem being worsened by global warming. QTLs for tolerance to high temperature during ripening must be identified in order to develop new cultivars efficiently. Here, we developed recombinant inbred lines (RILs) from crosses between the high-temperature-tolerant 'Genkitsukushi' and the high-temperature-sensitive 'Tsukushiroman'. The occurrence of white-back grains is significantly lower in 'Genkitsukushi' than in 'Tsukushiroman'. We evaluated their high-temperature tolerance and performed quantitative trait locus (QTL) analysis. A QTL for white-back grains on chromosome (chr.) 6 and a large-effect QTL on chr. 8 were identified in the two-year experiments. The QTL on chr. 8 was close to one we previously detected using RILs derived from 'Chikushi 52' × 'Tsukushiroman'. The results indicate that the QTL on chr. 6 is unique to 'Genkitsukushi' × 'Tsukushiroman', and that on chr. 8 could be identical between 'Genkitsukushi' and 'Chikushi 52'. Backcrossed lines which harbor the QTL region on chr. 8 of 'Genkitsukushi' in the background of 'Tsukushiroman' verified its effects. We also analyzed the marker genotypes near the QTLs on chr. 6 and 8 in relatives of 'Genkitsukushi'. We discuss the interaction between these QTLs and their relationship with high-temperature tolerance. [ABSTRACT FROM AUTHOR]

Published
2023
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22. A Trial for the Identification of Brown Planthopper (Nilaparvata lugens Stål) Resistance Alleles in Two Rice Lines, Norin-PL3 and Norin-PL4, Using Next-generation Sequencing and Simple Graphical Genotyping Methods

Author

NAKATSUJI, Yukina, primary, FUKUOKA, Shuichi, additional, KATAYOSE, Yuichi, additional, MIZUBAYASHI, Tatsumi, additional, SEZUTSU, Hideki, additional, KOBAYASHI, Tetsuya, additional, HATAKEYAMA, Yoshinori, additional, and TAMURA, Yasumori, additional

Published
2021
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23. Additional file 1 of Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars

Author

Hori, Kiyosumi, Keitaro Suzuki, Ishikawa, Haruka, Nonoue, Yasunori, Nagata, Kazufumi, Fukuoka, Shuichi, and Tanaka, Junichi

Subjects
food and beverages
Abstract

Additional file 1: Figure S1. Eating quality score, amylose content, protein content, stickiness of the surface of cooked rice grains, hardness of whole cooked rice grains and whiteness of rice grains in all chromosome segment substitution lines in the ‘Koshihikari’ genetic background in 2016 (upper) and 2017 (middle), and in the ‘Takanari’ genetic background in 2018 (lower). Data for eating quality traits are presented as means ± SD (n = 6).

Published
2021
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24. Genetic Elucidation for Response of Flowering Time to Ambient Temperatures in Asian Rice Cultivars

Author

Hori, Kiyosumi, Saisho, Daisuke, Nagata, Kazufumi, Nonoue, Yasunori, Uehara-Yamaguchi, Yukiko, Kanatani, Asaka, Shu, Koka, Hirayama, Takashi, Yonemaru, Jun-Ichi, Fukuoka, Shuichi, Mochida, Keiichi, Hori, Kiyosumi, Saisho, Daisuke, Nagata, Kazufumi, Nonoue, Yasunori, Uehara-Yamaguchi, Yukiko, Kanatani, Asaka, Shu, Koka, Hirayama, Takashi, Yonemaru, Jun-Ichi, Fukuoka, Shuichi, and Mochida, Keiichi

Abstract

Climate resilience of crops is critical for global food security. Understanding the genetic basis of plant responses to ambient environmental changes is key to developing resilient crops. To detect genetic factors that set flowering time according to seasonal temperature conditions, we evaluated differences of flowering time over years by using chromosome segment substitution lines (CSSLs) derived from japonica rice cultivars "Koshihikari" x "Khao Nam Jen", each with different robustness of flowering time to environmental fluctuations. The difference of flowering times in 9 years' field tests was large in "Khao Nam Jen" (36.7 days) but small in "Koshihikari" (9.9 days). Part of this difference was explained by two QTLs. A CSSL with a "Khao Nam Jen" segment on chromosome 11 showed 28.0 days' difference; this QTL would encode a novel flowering-time gene. Another CSSL with a segment from "Khao Nam Jen" in the region around Hd16 on chromosome 3 showed 23.4 days" difference. A near-isogenic line (NIL) for Hd16 showed 21.6 days' difference, suggesting Hd16 as a candidate for this QTL. RNA-seq analysis showed differential expression of several flowering-time genes between early and late flowering seasons. Low-temperature treatment at panicle initiation stage significantly delayed flowering in the CSSL and NIL compared with "Koshihikari". Our results unravel the molecular control of flowering time under ambient temperature fluctuations.

Published
2021

29. Identification of chromosome regions for high-temperature tolerance in the japonicarice cultivar ‘Genkitsukushi’ (Oryza sativaL.)

Author

Miyahara, Katsunori, Wada, Takuya, Fukuoka, Shuichi, Miyazaki, Masayuki, Yamaguchi, Osamu, Ishibashi, Masafumi, Kondo, Motohiko, Hamaoka, Norimitsu, and Ishibashi, Yushi

Abstract

ABSTRACTDegradation of the appearance of rice grains due to high temperatures during ripening is a serious problem being worsened by global warming. QTLs for tolerance to high temperature during ripening must be identified in order to develop new cultivars efficiently. Here, we developed recombinant inbred lines (RILs) from crosses between the high-temperature-tolerant ‘Genkitsukushi’ and the high-temperature-sensitive ‘Tsukushiroman’. The occurrence of white-back grains is significantly lower in ‘Genkitsukushi’ than in ‘Tsukushiroman’. We evaluated their high-temperature tolerance and performed quantitative trait locus (QTL) analysis. A QTL for white-back grains on chromosome (chr.) 6 and a large-effect QTL on chr. 8 were identified in the two-year experiments. The QTL on chr. 8 was close to one we previously detected using RILs derived from ‘Chikushi 52’ × ‘Tsukushiroman’. The results indicate that the QTL on chr. 6 is unique to ‘Genkitsukushi’ × ‘Tsukushiroman’, and that on chr. 8 could be identical between ‘Genkitsukushi’ and ‘Chikushi 52’. Backcrossed lines which harbor the QTL region on chr. 8 of ‘Genkitsukushi’ in the background of ‘Tsukushiroman’ verified its effects. We also analyzed the marker genotypes near the QTLs on chr. 6 and 8 in relatives of ‘Genkitsukushi’. We discuss the interaction between these QTLs and their relationship with high-temperature tolerance.

Published
2023
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35. Conversion effect of Hd1, Hd16, and Hd18 on the heading date of the rice line “Tohoku 206”, which has high temperature tolerance during the ripening stage

Author

Ishimori, Yuki, primary, Saeki, Ken-ichi, additional, Endo, Takashi, additional, Nakagomi, Yusuke, additional, Sato, Hiroko, additional, Mizobuchi, Ritsuko, additional, Taguchi-‍Shiobara, Fumio, additional, Fukuoka, Shuichi, additional, Yamanouchi, Utako, additional, Ando, Tsuyu, additional, and Mizubayashi, Tatsumi, additional

Published
2020
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41. Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross

Author

Nagata, Kazufumi, Ando, Tsuyu, Nonoue, Yasunori, Mizubayashi, Tatsumi, Kitazawa, Noriyuki, Shomura, Ayahiko, Matsubara, Kazuki, Ono, Nozomi, Mizobuchi, Ritsuko, Shibaya, Taeko, Ogiso-Tanaka, Eri, Hori, Kiyosumi, Yano, Masahiro, and Fukuoka, Shuichi

Subjects
Oryza sativa L, quantitative trait loci (QTL), fungi, grain shape, food and beverages, advanced mapping population, chromosome segment substitution lines (CSSLs), Research Paper
Abstract

Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC4F2 lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population. Only 8 QTLs for grain length or grain width were detected in the F2 population, versus 47 in the CSSL population and 65 in the BC4F2 population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.

Published
2015

42. Natural Variation in the Flag Leaf Morphology of Rice Due to a Mutation of the NARROW LEAF 1 Gene in Oryza sativa L

Author

TAGUCHI-SHIOBARA, Fumio, OTA, Tatsuya, EBANA, Kaworu, OOKAWA, Taiichiro, YAMASAKI, Masanori, TANABATA, Takanari, YAMANOUCHI, Utako, WU, Jianzhong, ONO, Nozomi, NONOUE, Yasunori, NAGATA, Kazufumi, FUKUOKA, Shuichi, HIRABAYASHI, Hideyuki, YAMAMOTO, Toshio, YANO, Masahiro, Fumio, TAGUCHI-SHIOBARA, Tatsuya, OTA, Kaworu, EBANA, Taiichiro, OOKAWA, Masanori, YAMASAKI, Takanari, TANABATA, Utako, YAMANOUCHI, Jianzhong, WU, Nozomi, ONO, Yasunori, NONOUE, Kazufumi, NAGATA, Shuichi, FUKUOKA, Hideyuki, HIRABAYASHI, Toshio, YAMAMOTO, and Masahiro, YANO

Subjects
Genotype, Quantitative Trait Loci, flag leaf width, Genetically modified crops, Investigations, Quantitative trait locus, Japonica, Genetics, natural variation, Oryza sativa L, Allele, Gene, Alleles, Plant Proteins, Oryza sativa, biology, rice, Chromosome Mapping, food and beverages, Oryza, Plants, Genetically Modified, biology.organism_classification, Plant Leaves, Phenotype, Chromosome 4, Mutation, Mutation (genetic algorithm), NARROW LEAF 1, Genome-Wide Association Study
Abstract

We investigated the natural variations in the flag leaf morphology of rice. We conducted a principal component analysis based on nine flag leaf morphology traits using 103 accessions from the National Institute of Agrobiological Sciences Core Collection. The first component explained 39% of total variance, and the variable with highest loading was the width of the flag leaf (WFL). A genome-wide association analysis of 102 diverse Japanese accessions revealed that marker RM6992 on chromosome 4 was highly associated with WFL. In analyses of progenies derived from a cross between Takanari and Akenohoshi, the most significant quantitative trait locus (QTL) for WFL was in a 10.3-kb region containing the NARROW LEAF 1 (NAL1) gene, located 0.4 Mb downstream of RM6992. Analyses of chromosomal segment substitution lines indicated that a mutation (G1509A single-nucleotide mutation, causing an R233H amino acid substitution in NAL1) was present at the QTL. This explained 13 and 20% of total variability in WFL and the distance between small vascular bundles, respectively. The mutation apparently occurred during rice domestication and spread into japonica, tropical japonica, and indica subgroups. Notably, one accession, Phulba, had a NAL1 allele encoding only the N-terminal, or one-fourth, of the wild-type peptide. Given that the Phulba allele and the histidine-type allele showed essentially the same phenotype, the histidine-type allele was regarded as malfunctional. The phenotypes of transgenic plants varied depending on the ratio of histidine-type alleles to arginine-type alleles, raising the possibility that H233-type products function differently from and compete with R233-type products.

Published
2015

50. Precise estimation of genomic regions controlling lodging resistance using a set of reciprocal chromosome segment substitution lines in rice

Author

Ookawa, Taiichiro, primary, Aoba, Ryo, additional, Yamamoto, Toshio, additional, Ueda, Tadamasa, additional, Takai, Toshiyuki, additional, Fukuoka, Shuichi, additional, Ando, Tsuyu, additional, Adachi, Shunsuke, additional, Matsuoka, Makoto, additional, Ebitani, Takeshi, additional, Kato, Yoichiro, additional, Mulsanti, Indria Wahyu, additional, Kishii, Masahiro, additional, Reynolds, Matthew, additional, Piñera, Francisco, additional, Kotake, Toshihisa, additional, Kawasaki, Shinji, additional, Motobayashi, Takashi, additional, and Hirasawa, Tadashi, additional

Published
2016
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