Identification of a Candidate Gene for Panicle Length in Rice (Oryza sativa L.) Via Association and Linkage Analysis

Liu, Erbao; Liu, Yang; Wu, Guocan; Zeng, Siyuan; Thi, Thu Giang Tran; Liang, Lijun; Yh, Liang; Zhang, Dong; She, Dong; Wang, Hui; Zaid, Imdad Ullah; Hong, Delin

doi:10.3389/fpls.2016.00596

Cited by 57 publications

(43 citation statements)

References 69 publications

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“…Out of them, five SSR loci were in aggrement to the previous studies. Previous reports indicated that the markers RM154, RM551, RM5711, RM234 and RM19 were associated with grain yield QTLs, (Table 5) viz., qYLD2.1 & qts1 , qYLD-4 & qPL-4.1, qYLD-7.1 , and qYLD-12.1, qSpn-12.1 , respectively [12,25,26,30,59,87]. Similarly, the marker RM5709 has been well documented in the www.gramene.org database for its association with grain yield QTL.…”

Section: Discussionmentioning

confidence: 99%

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

Donde

Mohapatra

Baksh

et al. 2020

Preprint

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16A panel of 60 genotypes consisting of New Plant Types (NPTs) along with indica, tropical and 17 temperate japonica genotypes were phenotypically evaluated for four seasons in irrigated situation 18 for grain yield per se and component traits. Twenty NPT genotypes were found to be promising with 19 an average grain yield of 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to 20 identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were 21 found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A 22 moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 23 8% within genotypes, 68% among the genotypes within the population and 24% among the 24 populations were observed (AMOVA). The association analysis using GLM and MLM models led to 25 the identification of 30 and 10 SSR markers were associated with 70 and 16 QTLs, respectively. 26 Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely, 27 tiller number (qTL-6. 29 total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight 30 qTGW-8.1 ), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, 31 qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se 11.1). This information could be useful for identification of highly potential parents for development 33 of transgressive segregants. Moreover, super rice genotypes could be developed through pyramiding 34 of these QTLS for important yield traits for prospective increment in yield potentiality and breaking 35 yield ceiling. 36 Introduction 39Rice (Oryza sativa L.) is a staple crop for more than 3.5 billion people in the globe. In current 40 scenario, rice productivity is increasing rate at 1% per year which is less than the 2.4% per year rate 41 required to double the global production by 2050 [1]. Considering a glimpse of the history, a 42 quantum jump in productivity was achieved due to the green revolution in mid-sixties, which 43 drastically enhanced the rice production of the world. However, a ceiling of productivity potentiality 44 is reported by and large in semi-dwarf inbred indica genotypes since release of , in spite of 45 substantial improvement in yield stability, per day productivity and grain quality [3]. A 46 breakthrough in productivity barrier is necessitated because of increasing competition for natural 47 resources viz., land, water and others given population explosion coupled with expanding 48 industrialization, urbanization and diversion of agricultural land [1,4,5]. This is still aggravated with 49 the abnormal change in weather and climate with significant influence on crop productivity and 50 quality [6,7]. 51Rice scientists are facing many challenges for doubling rice production by 2050. Irrigated 52 rice has a share of 75% of total rice production in the world, although it has a share of about 55% of 53 the total rice area [2]. Therefore, improveme...

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Section: Discussionmentioning

confidence: 99%

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

Donde

Mohapatra

Baksh

et al. 2020

Preprint

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“…QTL of PL is mapped with difficultly in individual plants, because it is a typical quantitative trait controlled by multiple genes and influenced by the environment, plasticity (Adriani et al, ), susceptibility to the confounding panicle structure (Crowell et al, ) and large‐amplitude variation in PL within a plant or between individuals with the same genotype (Xie et al, ). As a result, the number and effect of the QTLs for PL detected via linkage mapping may differ amongst different populations (Liu et al, ), which explains why we can obtain different effects values of a PL QTL identified and mapped in different replications.…”

Section: Discussionmentioning

confidence: 99%

“…PL QTL is commonly co‐identified with heading date (Liu et al, ). Growth‐Regulating Factor 4 ( OsGRF4 ) controls synchronously PL, grain shape and seed shattering in rice by regulating two cytokinin dehydrogenase precursor genes ( CKX5 and CKX1 ) resulting in increased cytokinin level (Sun et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…To identify QTLs or HQTLs, the average phenotypic means of genotypic class SSSLs or F 1 and donor HJX74 were compared through the ANOVA feature by t test significant difference with three replicates (Liu et al, ), and interval analysis ( p < 0.01 and/or LOD threshold ≥ 2.5) was conducted for markers within the target region using the spss 18.0 statistical software package and QTL IciMapping. The QTLs were named in accordance with Lander et al ().…”

Section: Methodsmentioning

confidence: 99%

“…PL is inherited quantitatively and controlled by major and minor quantitative trait loci (QTLs). To date, at least 253 QTLs for PL have been detected that are distributed across 12 chromosomes (Liu et al, ), such as DEP1 , SP1 , OsSPL14 , LP , qPL6 and PL (Cho et al, ; Hittalmani, Huang, Courtois, & Shashidhar, ; Huang et al, ; Kobayashi, Fukuta, Sato, Osaki, & Khush, ; Li et al, ; Liu et al, ; Mei et al, ; Miura et al, ; Zhang et al, ). However, only a few genes have been cloned and applied in rice plant architecture breeding.…”

Section: Introductionmentioning

confidence: 99%

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Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa) through single‐segment substitution lines

et al. 2019

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Panicle length (PL), an important yield‐related trait, strongly affects yield components, such as grain number, grain density and rice quality. More than 200 panicle length quantitative trait loci (PL QTLs) are identified, but only a small number are applied in rice breeding. In this study, we performed QTL analysis for PL using 42 single‐segment substitution lines (SSSLs) derived from nine donors in the genetic background of HJX74. Fourteen QTLs and five heterosis QTLs (HQTLs) for PL were recognised. Three QTLs and four HQTLs acted positively, and the other eleven QTLs and one HQTL acted negatively. By scanning the single heterozygous background region of the F2 population with large‐genetic‐effect SSSLs, we mapped PL loci qPL6‐2 and qPL7‐1 to different locations on chromosomes 6 and 7, respectively, in three consecutive years of independent trials. The genetic effects of these QTLs were further assessed. qPL6‐2 demonstrated the most positive additive effect (QTL), whereas qPL7‐1 achieved the most positive dominant effect (HQTL) for PL. These results indicated that the pyramiding of PL QTLs might increase grain yield and facilitate the application of the beneficial allele in hybrid rice breeding.

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Diversity of Panicle Architecture and Traits Influencing Grain Filling

Mohapatra

Sahu

2021

Panicle Architecture of Rice and Its Relationship With Grain Filling

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In the long history of domestication through cultivation and selection under diverse habitats; the plant acquired adaptability for growth matching with the physico-chemical behavior of the environment, which is most prominently reflected in the phenology of panicle. Panicle morphology varies significantly more than any other phenotypic attribute of the plant and it is both cultivar and environmentspecific. The architectural traits, including branching, panicle length, and spikelet number, are established during the reproductive phase from panicle initiation to heading depending on activities rachis and branch meristems. Termination of rachis meristem activity fixes primary branch number, whereas, the transition of the primary or secondary meristem into spikelet limits spikelet number; the earlier the closure of the events less are the numbers. Many genes, either small effects or major effects, have been identified that are associated with panicle architecture and grain yield. They are distributed across the 12 rice chromosomes.

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Identification of a Candidate Gene for Panicle Length in Rice (Oryza sativa L.) Via Association and Linkage Analysis

Cited by 57 publications

References 69 publications

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa) through single‐segment substitution lines

Diversity of Panicle Architecture and Traits Influencing Grain Filling

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