The <i>SEEDLING BIOMASS 1</i> allele from <i>indica</i> rice enhances yield performance under low‐nitrogen environments

Xu, Jing; Shang, Lei; Wang, Jiajia; Chen, Minmin; Xue, Fu Shan; He, Huiying; Wang, Zian; Zhu, Li; Hu, Jiang; Zhang, Chao; Chen, Guang; Gao, Zhenyu; Zou, Weiwei; Ren, Deyong; Shen, Lan; Zhang, Qiang; Li, Qing; Guo, Longbiao; Qian, Qian; Zhang, Guangheng

doi:10.1111/pbi.13642

Cited by 12 publications

(8 citation statements)

References 10 publications

(10 reference statements)

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“…For example, HapC of ARE1 carried by XI accession 9311 contained several variations in the 5′UTR that was different from reported variations, including a 7,808-bp insertion at position −466 in this study ( Supplementary Table S10 ) and a 6-bp insertion at position −314 in reported study ( Wang Q. et al, 2018 ). HapD of SBM1 was carried by 14 out of 36 accessions in this study ( Supplementary Table S5 ), but was not identified from 1,140 rice accessions of broad genetic diversity ( Xu et al, 2021 ). Therefore, high-quality genomic sequence was of great importance in haplotype analysis.…”

Section: Discussionmentioning

confidence: 85%

“…For SBM1 , four haplotypes were identified, including the three types reported by Xu et al (2021 ; Table 2 and Supplementary Table S5 ). HapA and HapB were distributed mainly in GJ and cA accessions, respectively, while both HapC and HapD were distributed mainly in XI accessions.…”

Section: Resultsmentioning

confidence: 99%

“…SBM1 was reported as a negative regulator of NUE and grain yield, and the elite type HapB carried by accession Kasalath was a type with weak function ( Xu et al, 2021 ). HapD carried a 1,204-bp deletion in the 5′UTR region and a non-synonymous SNP at position + 2 that would disrupt the translation start site, and was likely to have a better performance than HapB ( Supplementary Table S5 ).…”

Section: Resultsmentioning

confidence: 99%

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Development and Application of Intragenic Markers for 14 Nitrogen-Use Efficiency Genes in Rice (Oryza sativa L.)

Liu

et al. 2022

Front. Plant Sci.

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Asian cultivated rice consists of two main subspecies, xian/indica (XI) and geng/japonica (GJ), and GJ accessions have significantly lower nitrogen-use efficiency (NUE) than XI accessions. In order to facilitate genetic improvement of NUE in GJ accessions, we conducted haplotype analysis of 14 cloned NUE genes using 36 rice germplasm accessions with high-quality reference genome and developed 18 intragenic markers for elite haplotypes, which were then used to evaluate NUE genes in another 41 genetically diverse germplasm accessions from 12 countries and 71 approved GJ cultivars from northern provinces of China. Our results show that elite haplotypes of 12 NUE genes are mainly existed in XI accessions, but few is distributed in GJ accessions. The number of elite haplotypes carried by an XI accession can reach 10, while that carried by a GJ accession is less than 3. Surprisingly, the elite haplotype of gene DEP1 is nearly fixed in approved GJ cultivars, and elite haplotypes of gene MYB61 and NGR5 have been introduced into some approved GJ cultivars. The developed intragenic markers for NUE genes and evaluated 77 genetically diverse rice accessions could be of great use in the improvement of NUE in GJ cultivars.

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Section: Discussionmentioning

confidence: 85%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Development and Application of Intragenic Markers for 14 Nitrogen-Use Efficiency Genes in Rice (Oryza sativa L.)

Liu

et al. 2022

Front. Plant Sci.

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“…NAL1 and the gain-of-function mutation dep1-1 have been reported to play important roles in N-responsive tillering regulation, and pyramiding of the dep1-1 and NAL1 NJ6 alleles can achieve sustainable improvements in NUE and grain yield in japonica rice breeding ( Sun et al, 2014 ; Xu et al, 2019 ). The introgression of favorable alleles of other NUE-related genes such as OsTCP19 and OsSBM1 also showed great potential for genetic improvement of high NUE in rice ( Liu et al, 2021 ; Xu et al, 2021 ).…”

Section: Introgression Lines Are Valuable Resources For Rice Breedingmentioning

confidence: 99%

Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice (Oryza sativa L.)

Zhang

et al. 2022

Front. Plant Sci.

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The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.

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“…On the other hand, pleiotropic genes controlling grain number, plant height, and heading date have been cloned, such as Ghd7, Ghd7.1, Ghd8, and Ghd2 [11][12][13][14]. Recently, the qSBM1 was reported to increase plant height and biomass aboveground, resulting in enhanced grain number per panicle, grain yield per plant, and nitrogen efficiency [15]. In view of the limited number of cloned loci, investigating new stable plant height QTLs is a pressing demand in rice.…”

Section: Introductionmentioning

confidence: 99%

Finding Stable QTL for Plant Height in Super Hybrid Rice

Yang

Kang

et al. 2022

Agriculture

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Plant height (PH) is one of the most important agronomic traits determining plant architecture in rice. To investigate the genetic basis of plant height in the high-yielding hybrid rice variety Nei2You No.6, recombinant inbred sister lines (RISLs) were used to map quantitative trait loci (QTL) over four years. A total of 19 minor/medium-effect QTLs were mapped on eleven chromosomes except chromosome 10, totally explaining 44.61–51.15% phenotypic variance in four environments. Among these, qPH-1a, qPH-1b, qPH-2b, qPH-3b, qPH-6, and qPH-7b were repeatedly detected over four years. Among these, the qPH-6 was mapped to an interval of 22.11–29.41 Mb on chromosome 6L, which showed the highest phenotypic variation explained (PVE) of 10.22–14.05% and additive effect of 3.45–4.63. Subsequently, evaluation of near isogenic lines (NILs) showed that the qPH-6 allele from the restorer line (R8006) could positively regulate plant height, resulting in an 18.50% increase in grain yield. These results offered a basis for further mapping of qPH-6 and molecular breeding in improving plant architecture in rice.

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The SEEDLING BIOMASS 1 allele from indica rice enhances yield performance under low‐nitrogen environments

Cited by 12 publications

References 10 publications

Development and Application of Intragenic Markers for 14 Nitrogen-Use Efficiency Genes in Rice (Oryza sativa L.)

Development and Application of Intragenic Markers for 14 Nitrogen-Use Efficiency Genes in Rice (Oryza sativa L.)

Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice (Oryza sativa L.)

Finding Stable QTL for Plant Height in Super Hybrid Rice

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