Identification of QTLs for high grain yield and component traits in new plant types of rice

Donde, Ravindra; Mohapatra, SD; Baksh, Shamim; Padhy, Barada; Mukherjee, Mitadru; Roy, Somnath; Chattopadhyay, Krishnendu; Anandan, A.; Swain, Padmini; Sahoo, Khirod Kumar; Singh, O. N.; Behera, Lambodar; Dash, Sushanta Kumar

doi:10.1371/journal.pone.0227785

Cited by 27 publications

(10 citation statements)

References 85 publications

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“…Fifty-six of 78 markers exhibited polymorphism (73%), which gave rise to 154 alleles, less than in our previous study 30 . We obtained 128 alleles from 39 polymorphic primers, and more than reported by Donde et al 31 , 154 alleles from 65 polymorphic markers. The present average of 2.7 alleles per locus was lower than that of many other research reports; for example, Noyer et al 32 analyzed 419 rice accessions using 16 SSR markers and reported an average of 9.1 alleles per locus.…”

Section: Discussionmentioning

confidence: 92%

Multi-trait association study identifies loci associated with tolerance of low phosphorus in Oryza sativa and its wild relatives

Anandan

Nagireddy

Sabarinathan

et al. 2022

Sci Rep

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We studied variation in adaptive traits and genetic association to understand the low P responses, including the symbiotic association of arbuscular mycorrhizal (AM) fungal colonization in Oryza species (O. sativa, O. nivara, and O. rufipogon). In the present experiment, we performed the phenotypic variability of the morphometric and geometric traits for P deficiency tolerance and conducted the association studies in GLM and MLM methods. A positive association between the geometric trait of the top-view area and root traits suggested the possibility of exploring a non-destructive approach in screening genotypes under low P. The AMOVA revealed a higher proportion of variation among the individuals as they belonged to different species of Oryza and the NM value was 2.0, indicating possible gene flow between populations. A sub-cluster with superior-performing accessions had a higher proportion of landraces (42.85%), and O. rufipogon (33.3%) was differentiated by four Pup1-specific markers. Association mapping identified seven notable markers (RM259, RM297, RM30, RM6966, RM242, RM184, and PAP1) and six potential genotypes (IC459373, Chakhao Aumbi, AC100219, AC100062, Sekri, and Kumbhi Phou), which will be helpful in the marker-assisted breeding to improve rice for P-deprived condition. In addition, total root surface area becomes a single major trait that helps in P uptake under deficit P up to 33% than mycorrhizal colonization. Further, the phenotypic analysis of the morphometric and geometric trait variations and their interactions provides excellent potential for selecting donors for improving P-use efficiency. The identified potential candidate genes and markers offered new insights into our understanding of the molecular and physiological mechanisms driving PUE and improving grain yield under low-P conditions.

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Section: Discussionmentioning

confidence: 92%

Multi-trait association study identifies loci associated with tolerance of low phosphorus in Oryza sativa and its wild relatives

Anandan

Nagireddy

Sabarinathan

et al. 2022

Sci Rep

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“…Association mapping has shown great promise and power of mapping the complex quantitative traits in plants as compared to traditional bi-parental mapping. Several scientists employed GWAS in the rice population panel for various traits and reported novel QTLs (Suman et al 2020;Haritha et al 2020;Donde et al 2020;Pradhan et al 2019Pradhan et al , 2020Zhang et al 2014Zhang et al , 2019Norton et al 2018;Kadam et al 2018;Juan et al 2018;Prasanth et al 2017;Swamy et al 2017;Xu et al 2016;Lu et al 2015;Zhao et al 2011;Borba et al 2010;Agrama et al 2007). But such study in diverse rice landrace is very meager.…”

Section: Discussionmentioning

confidence: 99%

“…However, linkage mapping approach does not sample the larger pool of genetic variation that may contribute to phenotypic variation within a species. In addition to the bi-parental mapping strategies used in QTL mapping of important agronomic and nutritional traits, GWAS is widely used in the recent times (Suman et al 2020;Haritha et al 2020;Donde et al 2020;Pradhan et al 2019Pradhan et al , 2020Zhang et al 2014Zhang et al , 2019Norton et al 2018;Kadam et al 2018;Juan et al 2018;Prasanth et al 2017;Swamy et al 2017;Xu et al 2016;Lu et al 2015;Zhao et al 2011;Borba et al 2010;Agrama et al 2007). GWAS maximizes the utilization of genetic variation of unrelated individuals in the natural population for large and more representative set of loci without the additional requirement of mapping population development (Kadam et al 2018;Swamy et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association mapping revealed numerous novel genomic loci for grain nutritional and yield-related traits in rice (Oryza sativa L.) landraces

et al. 2020

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A core set of 190 rice landraces were used to decipher the genetic structure and to discover the chromosomal regions containing QTLs, affecting the grain micro-nutrients, fatty acids, and yield-related traits by using 148 molecular markers in this study. Landraces were categorized into three sub-groups based on population stratification study and followed by neighborjoining tree and principal component analysis. Analysis of variance revealed abundant variations among the landraces for studied traits with less influence of environmental factors. Genome Wide Association Studies (GWAS) revealed 22 significant and consistent QTLs through marker trait association (MTAs) for 12 traits based on 2 years and pooled analysis. Out of 22 QTLs, three have been reported earlier while 19 QTLs are novel. Interestingly, 13 QTLs out of 22 were explained more than 10% phenotypic variance. Association of RM1148 and RM205 with Days to 50% flowering was comparable with flowering control genes Ghd8/qDTH8 and qDTH9, respectively. Similarly, Zn content was associated with RM44, which is situated within the QTL qZn8-1. Moreover, significant association of RM25 with oleic acid content was closely positioned with QTL qOle8. Association of RM7434 with grain yield/plant; RM184 with spikelet fertility %; R3M10, R9M42 with hundred seed weight; RM536, RM17467, RM484, RM26063 with Fe content; RM44, RM6839 with Zn content are the major outcomes of this study. In addition, association of R11M23 with days to 50% flowering, panicle length and total spikelets per panicle are explained the possible occurrence of pleiotropism among these traits. Prominent rice landraces viz., Anjani (early maturity); Sihar (extra dwarf); Gangabaru (highest grain yield/plant); Karhani (highest iron content); Byalo-2 (highest zinc content) and Kadamphool (highest oleic acid) were identified through this study. The present study will open many avenues towards utilization of these QTLs and superior landraces in rice breeding for developing nutrition-rich high yielding varieties.

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“…In addition, higher activity of the SBI significantly reduced the rice PH, and, therefore, its application in rice production contributed to breed improved lodging-resistant rice varieties and thus increased yield. Although several studies on associations between markers and the plant height have been conducted in rice [ 10 , 30 , 31 , 32 , 33 ], to date, no report has documented a QTL analysis of the relationships between plant height and its components traits (panicle length and the length of all internodes), using two mapping strategies.…”

Section: Introductionmentioning

confidence: 99%

Detection of QTLs for Plant Height Architecture Traits in Rice (Oryza sativa L.) by Association Mapping and the RSTEP-LRT Method

Sitoe

Zhang

Chen

et al. 2022

Plants

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Plant height (PH) and its component traits are critical determinants of lodging resistance and strongly influence yield in rice. The genetic architecture of PH and its component traits were mined in two mapping populations. In the natural population composed of 504 accessions, a total of forty simple sequence repeat (SSR) markers associated with PH and its component traits were detected across two environments via association mapping. Allele RM305-210 bp on chromosome 5 for PH had the largest phenotypic effect value (PEV) (−51.42 cm) with a reducing effect. Allele RM3533-220 bp on chromosome 9 for panicle length and allele RM264-120 bp on chromosome 8 for the length of upper first elongated internode (1IN) showed the highest positive PEV. Among the elongated internodes with negative effects being desirable, the allele RM348-130 bp showed the largest PEV (−7.48 cm) for the length of upper second elongated internode. In the chromosome segment substitution line population consisting of 53 lines, a total of nine QTLs were detected across two environments, with the phenotypic variance explained (PVE) ranging 10.07–28.42%. Among the detected QTLs, q1IN-7 explained the largest PVE (28.42%) for the 1IN, with an additive of 5.31 cm. The favorable allele RM257-125 bp on chromosome 9 for the 1IN increasing was detected in both populations. The favorable alleles provided here could be used to shape PH architecture against lodging.

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Identification of QTLs for high grain yield and component traits in new plant types of rice

Cited by 27 publications

References 85 publications

Multi-trait association study identifies loci associated with tolerance of low phosphorus in Oryza sativa and its wild relatives

Multi-trait association study identifies loci associated with tolerance of low phosphorus in Oryza sativa and its wild relatives

Genome-wide association mapping revealed numerous novel genomic loci for grain nutritional and yield-related traits in rice (Oryza sativa L.) landraces

Detection of QTLs for Plant Height Architecture Traits in Rice (Oryza sativa L.) by Association Mapping and the RSTEP-LRT Method

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