Genetic Analysis of Agronomic Traits and Grain Iron and Zinc Concentrations in a Doubled Haploid Population of Rice (Oryza sativa L.)

Calayugan, Mark Ian C.; Formantes, Andrea Kariza; Amparado, Amery; Descalsota-Empleo, Gwen Iris; Nha, Chau Thanh; Inabangan-Asilo, Mary Ann; Swe, Zin Mar; Hernandez, Jose E.; Borromeo, Teresita H.; Lalusin, Antonio G.; Mendioro, Merlyn S.; Diaz, Ma. Genaleen Q.; Viña, Celia B. Dela; Reinke, Russell; Swamy, B. P. Mallikarjuna

doi:10.1038/s41598-020-59184-z

Cited by 60 publications

(44 citation statements)

References 63 publications

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“…On CaLG05, QTLs CaqFe 5.1- CaqZn 5.1 were colocalized within the SNP marker interval of SCA5_37174786-SCA5_35312501. Previous studies have reported QTL colocalization for micronutrient concentration in chickpea on chromosomes 4, 5, and 7 ( 2 ) and also in rice ( 10 ). Hence, these genomic regions on chromosome 4 may contain conserved QTLs for seed Fe and Zn concentrations across diverse genetic backgrounds.…”

Section: Discussionmentioning

confidence: 99%

“…Pleiotropy or tight linkage of genes controlling multiple traits may be the reason for the colocalization of QTLs ( 50 ). These regions with colocated QTLs will be useful for simultaneous improvement using marker-assisted selection ( 10 ).…”

Section: Discussionmentioning

confidence: 99%

“…Biofortification of staple crops through plant breeding is a highly cost-effective and long-term strategy to enhance micronutrient density in crop plants ( 6 ). Efforts in this direction have involved understanding the genetic architecture of Fe and Zn concentrations in seeds of cereals crops ( 7 – 10 ). More recently, the focus has been on pulses that serve as secondary staples, mainly because of their increased protein content ( 11 ).…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea (Cicer arietinum L.)

et al. 2020

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Biofortification through plant breeding is a cost-effective and sustainable approach towards addressing micronutrient malnutrition prevailing across the globe. Screening cultivars for micronutrient content and identification of quantitative trait loci (QTLs)/genes and markers help in the development of biofortified varieties in chickpea ( Cicer arietinum L.). With the aim of identifying the genomic regions controlling seed Fe and Zn concentrations, the F 2:3 population derived from a cross between MNK-1 and Annigeri 1 was genotyped using genotyping by sequencing approach and evaluated for Fe and Zn concentration. An intraspecific genetic linkage map comprising 839 single nucleotide polymorphisms (SNPs) spanning a total distance of 1,088.04 cM with an average marker density of 1.30 cM was constructed. By integrating the linkage map data with the phenotypic data of the F 2:3 population, a total of 11 QTLs were detected for seed Fe concentration on CaLG03, CaLG04, and CaLG05, with phenotypic variation explained ranging from 7.2% ( CaqFe3.4 ) to 13.4% ( CaqFe4.2 ). For seed Zn concentration, eight QTLs were identified on CaLG04, CaLG05, and CaLG08. The QTLs individually explained phenotypic variations ranging between 5.7% ( CaqZn8.1 ) and 13.7% ( CaqZn4.3 ). Three QTLs for seed Fe and Zn concentrations ( CaqFe4.4, CaqFe4.5 , and CaqZn4.1 ) were colocated in the “ QTL-hotspot ” region on CaLG04 that harbors several drought tolerance-related QTLs. We identified genes in the QTL regions that encode iron–sulfur metabolism and zinc-dependent alcohol dehydrogenase activity on CaLG03, iron ion binding oxidoreductase on CaLG04, and zinc-induced facilitator-like protein and ZIP zinc/iron transport family protein on CaLG05. These genomic regions and the associated markers can be used in marker-assisted selection to increase seed Fe and Zn concentrations in agronomically superior chickpea varieties.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea (Cicer arietinum L.)

et al. 2020

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“…Crops are subjected to genotype by environment interaction (GxE) and to agronomic management practices. Environmental factors such as soil redox potential, pH, soil structure and texture, organic matter content and climate conditions, among others, influence GxE interaction and may affect rice zinc levels accumulation [102,103]. This is a consequence of the alteration of quantitative trait locus (QTL) responsible for the absorption and translocation of zinc to the grain in biofortified varieties [68].…”

Section: Plos Onementioning

confidence: 99%

The acceptance of zinc biofortified rice in Latin America: A consumer sensory study and grain quality characterization

et al. 2020

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Zinc deficiency is a major public health problem in vulnerable populations of Latin America and the Caribbean. Biofortification of rice (Oryza sativa L.) with zinc has the potential to alleviate zinc deficiencies. However, as plant breeding processes can alter grain culinary quality and favorable sensory attributes, grain quality and consumer acceptability need to be assessed prior to releasing a variety to the public. A grain quality characterization and a sensory acceptability analysis were carried out with two varieties of zinc biofortified rice and a local control both in Bolivia and Colombia. The aim of this study was to evaluate the physicochemical parameters that are significant in consumer acceptance and to determine the acceptability of zinc biofortified rice by consumers. Results of physicochemical parameters were analyzed using ANOVA. The sensory acceptability was evaluated in 243 adults utilizing a 7-point hedonic scale and a Wilcoxon’s signed rank test was used to determine the overall acceptability of the varieties. Biofortified rice variety T2-11 and MAC-18 -control 1- were equally accepted by consumers in Bolivia with no significant differences (p<0.05). The grain quality analysis reported that both presented long and slender rice grains (L>7.5 mm and L/B>3), an intermediate to high amylose content (>25%) and a similar level of chalkiness. In Colombia, the biofortified variety 035 presented a higher score in overall acceptance in comparison to biofortified variety 021 and the local variety CICA4 -control 2-. However, no significant differences were observed (p<0.05). Conversely to the other two varieties, the biofortified variety 035 presented the largest size grain (L/B = 2.97), a lower chalkiness and an amylose content above 25%. This study shows that the grain quality properties of rice have an influence on acceptability and that zinc biofortified rice varieties are accepted by consumers.

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“…Such non-segregating populations include doubled haploid lines (DHLs), near isogenic lines (NILs), recombinant inbred lines (RILs), chromosomal segment substitution lines (CSSLs). Among them the DHLs can be a very useful resource for identi cation of yield QTLs and heterosis associated loci [8,9,10,11,12], in the context of hybrid rice improvement. Development of the above mentioned immortal and xed populations from popular high-yielding rice hybrids could be a valuable resource for mapping various agronomically important traits relevant to hybrid rice [13,14].…”

Section: Introductionmentioning

confidence: 99%

QTL Mapping of Novel Genomic Regions for Yield Related Traits in Doubled Haploid (DH) Population Derived from the Popular Rice Hybrid KRH-2

Kulkarni

Ulaganathan

et al. 2020

Preprint

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Background: Rice, being the principal food crop and major nutritional source for more than half of the global population, is also an important source of livelihood in many South and South-East Asian countries. Amidst diminishing natural resources and many biotic-abiotic stresses, increasing the yield of rice varieties remains a challenging task. Identification of novel and yield augmenting alleles from stable rice hybrids is crucial to facilitate their marker-assisted transfer into various genetic backgrounds. Results: Quantitative trait loci (QTL) mapping using a population of 125 doubled haploid (DH) lines developed from the cross IR58025A/KMR3R and 126 polymorphic SSR; EST-derived SSR markers led to the identification of 12 each of major-minor effect QTLs for yield related traits. Major effect QTLs were detected for traits namely days to fifty percent flowering, test (1,000) grain weight, plant height, panicle weight, panicle length, flag leaf width, flag leaf length, biomass and total grain yield/plant explaining the phenotypic variability in the range of 29.95%-56.75%. QTL hotspots were detected on chromosome 3 for the traits, panicle length and total grain yield/plant and on chromosome 6 for the traits, panicle length, flag leaf length and total grain yield/plant. Though many of these QTLs were noted to co-localize with the QTL regions reported in earlier studies, five novel and major effect QTLs for panicle length, biomass, flag leaf width, panicle weight, plant height and three novel minor effect QTLs for panicle weight and fertile grains per panicle, were identified in this study. Conclusions: Through this study, both major-minor effect novel QTLs for crucial yield related traits, viz., fertile grains per panicle, panicle length, panicle weight were identified. Further, the QTL hotspots identified on two different chromosomes for flag leaf length, panicle length and total grain yield/plant shall not only help in understanding the underlying genetic mechanisms of yield regulation but also would provide an insight into the genetic synchrony among the various yield related traits in contributing for yield heterosis. The identified QTL hotspots after their validation can be deployed in breeding programs targeted towards improvement of yield heterosis.

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Genetic Analysis of Agronomic Traits and Grain Iron and Zinc Concentrations in a Doubled Haploid Population of Rice (Oryza sativa L.)

Cited by 60 publications

References 63 publications

Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea (Cicer arietinum L.)

Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea (Cicer arietinum L.)

The acceptance of zinc biofortified rice in Latin America: A consumer sensory study and grain quality characterization

QTL Mapping of Novel Genomic Regions for Yield Related Traits in Doubled Haploid (DH) Population Derived from the Popular Rice Hybrid KRH-2

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