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15 pages, 3504 KiB

Open AccessArticle

Large-Grain and Semidwarf Isogenic Rice Koshihikari Integrated with GW2 and sd1

by Motonori Tomita, Hideumi Ebata and Kohei Nakayama

Sustainability 2022, 14(17), 11075; https://doi.org/10.3390/su141711075 - 5 Sep 2022

Cited by 2 | Viewed by 2495

Intending to contribute to sustainable agriculture by “New Green Revolution,” we developed a large-grain/semidwarf isogenic line “Koshihikari sd1GW2” that incorporates both the large-grain gene GW2 and semidwarf gene sd1. GW2 homozygous B₃F₂ plant with the genomic background of Koshihikari was backcrossed twice with “Koshihikari sd1.” Koshihikari sd1GW2 fixed in BC₅F₃ was found to be 12.6 cm shorter than Koshihikari. Whole-genome sequencing proved one deletion in GW2 at 8,147,416 bp on chromosome 2 and the SNPs in sd1 at 38,267,510 bp on chromosome 1. The size of the DNA fragments integrated with each gene was determined as the distance between both ends of SNP clusters. Through the backcrossing from BC₄ to BC₅, the DNA fragment integrated with GW2 decreased by 148,139 bp. The thousand-grain weight of Koshihikari sd1GW2 (27.8 g) was 18% greater than that of Koshihikari (23.6 g), and the grain yield of Koshihikari sd1GW2 (42.6 kg/a) was 0.5% higher than that of Koshihikari (42.4 kg/a). Our results suggested that Koshihikari sd1GW2 will be less susceptible to lodging by typhoons, cyclones, and heavy rainfall, ordinarily a concern in heavier panicle weight cultivars. We successfully integrated GW2 with sd1 for the first time, specifically in the genome of the leading, globally produced Japonica cultivar Koshihikari. Full article

(This article belongs to the Special Issue Advance in Plant Breeding and Plant Biotechnology for Sustainable Agriculture)

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15 pages, 7545 KiB

Open AccessArticle

Isogenic Japonica Rice Koshihikari Integrated with Late Flowering Gene Hd16 and Semidwarfing Gene sd1 to Prevent High Temperature Maturation and Lodging by Typhoon

by Motonori Tomita and Ryotaro Tokuyama

Life 2022, 12(8), 1237; https://doi.org/10.3390/life12081237 - 15 Aug 2022

Cited by 1 | Viewed by 2772

Abstract

We developed semidwarf and late-maturing isogenics of Koshihikari to stabilize high yield and avoid high temperature maturation. Whole-genome analysis (WGS) was conducted to examine the transitional changes in the entire genome, the size of DNA fragments integrated with the target gene, and genes accompanying the target gene owing to the progress of backcrossing. In both Koshihikari Hd16 (BC₇F₄) and Koshihikari sd1Hd16 (BC₈F₂), an SNP from adenine to guanine was detected in Hd16 at 32,996,608 bp on chromosome 3, which is known to be a causative mutation of Hd16 in Nipponbare. In Koshihikari sd1Hd16 (BC₈F₂), an SNP from thymine to guanine was detected in sd1 at 38,267,510 bp on chromosome 1. From BC₇ to BC₈, the size of the DNA fragment integrated with Hd16 decreased by 5871 bp. Koshihikari sd1Hd16 flowered 12.1 days later than Koshishikari or Koshihikari sd1 did and was 14.2 cm (15%) shorter than Koshihikari. The yield in Koshishikari sd1Hd16 (63.2 kg/a) was 7.0% higher than that of Koshihikari. This is a new germplasm designed to avoid heat damage at ripening during high-temperature summer periods by late maturation owing to Hd16 as well as to avoid lodging by autumn typhoons by semidwarfness owing to sd1. Full article

(This article belongs to the Special Issue Cultivation and Regulation of Abiotic Stress for Field Crops)

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15 pages, 1919 KiB

Open AccessArticle

Identification and Validation of QTLs for Yield and Yield Components under Long-Term Salt Stress Using IR64 CSSLs in the Genetic Background of Koshihikari and Their Backcross Progenies

by Nguyen Sao Mai, Dao Duy Hanh, Mai Nakashima, Kotaro Kumamoto, Nguyen Thi Thu Thuy, Tohru Kobata, Kuniyuki Saitoh and Yoshihiko Hirai

Agriculture 2021, 11(8), 777; https://doi.org/10.3390/agriculture11080777 - 15 Aug 2021

Cited by 2 | Viewed by 3177

Abstract

Unraveling the complex genetic bases and mechanisms underlying salt tolerance is of great importance for developing salt-tolerant varieties. In this study, we evaluated 42 chromosome segment substitution lines (CSSLs) carrying chromosome segments from IR64 on the genetic background of Koshihikari under salt stress. Two CSSLs, SL2007 and SL2038, produced higher plant dry weight and grain yield than did Koshihikari under the stress condition. These CSSLs also showed lower Na⁺ and Cl⁻ accumulation in the leaf and whole plant at the full heading stage, which might be related to the higher grain yield and yield components. To understand the genetic control of its grain yield and yield components, a SL2007/Koshihikari F₂ population was generated for quantitative trait locus (QTL) analysis. Six QTLs for grain yield and yield-related traits were detected on chromosome 2. Using near-isogenic lines (NILs) from a SL2007/Koshihikari F₅ population, qSTGY2.2 was delimited to a 2.5 Mb region and novel qSTPN2 was delimited to a 0.6 Mb region. We also detected a novel QTL, qSTGF2, for grain filling, which was considered an important contributor to grain yield under salt stress in this CSSL. Our results provide insights into mechanisms conferring grain yield under salinity stress and new genetic resources for cloning and breeding. Full article

(This article belongs to the Topic Physiological and Molecular Characterization of Crop Tolerance to Abiotic Stresses)

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13 pages, 3325 KiB

Open AccessArticle

Genetic Elucidation for Response of Flowering Time to Ambient Temperatures in Asian Rice Cultivars

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

Int. J. Mol. Sci. 2021, 22(3), 1024; https://doi.org/10.3390/ijms22031024 - 20 Jan 2021

Cited by 8 | Viewed by 3062

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” × “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. Full article

(This article belongs to the Special Issue Molecular Research in Rice: Agronomically Important Traits 2.0)

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14 pages, 3760 KiB

Open AccessArticle

Identification of Rice Large Grain Gene GW2 by Whole-Genome Sequencing of a Large Grain-Isogenic Line Integrated with Japonica Native Gene and Its Linkage Relationship with the Co-integrated Semidwarf Gene d60 on Chromosome 2

by Motonori Tomita, Shiho Yazawa and Yoshimasa Uenishi

Int. J. Mol. Sci. 2019, 20(21), 5442; https://doi.org/10.3390/ijms20215442 - 31 Oct 2019

Cited by 4 | Viewed by 4138

Abstract

Genetic analysis of “InochinoIchi,” an exceptionally large grain rice variety, was conducted through five continuous backcrosses with Koshihikari as a recurrent parent using the large grain F₃ plant in Koshihikari × Inochinoichi as a nonrecurrent parent. Thorough the F₂ and all BCnF₂ generations, large, medium, and small grain segregated in a 1:2:1 ratio, indicating that the large grain is controlled by a single allele. Mapping by using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers with small grain homozygous segregants in the F₂ of Nipponbare × Inochinoichi, revealed linkage with around 7.7 Mb markers from the distal end of the short arm of chromosome 2. Whole-genome sequencing on a large grain isogenic Koshihikari (BC₄F₂) using next-generation sequencing (NGS) identified a single nucleotide deletion in GW2 gene, which is located 8.1 Mb from the end of chromosome 2, encoding a RING protein with E3 ubiquitin ligase activity. The GW2-integrated isogenic Koshihikari showed a 34% increase in thousand kernel weight compared to Koshihikari, while retaining a taste score of 80. We further developed a large grain/semi-dwarf isogenic Koshihikari integrated with GW2 and the semidwarfing gene d60, which was found to be localized on chromosome 2. The combined genotype secured high yielding while providing robustness to withstand climate change, which can contribute to the New Green Revolution. Full article

(This article belongs to the Special Issue Plant Genomics 2019)

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