Genetic architecture of maize yield traits dissected by QTL mapping and GWAS in maize

Xiao, Zhang; Ren, Zhiyong; Luo, Bowen; Zhong, Huan; Ma, Ping; Zhang, Hongkai; Hu, Hongmei; Wang, Yikai; Zhang, Haiying; Liu, Dan; Wu, Long‐Fei; Nie, Zhi; Zhu, Yonghui; He, Wei; Zhang, Suzhi; Su, Shunzong; Shen, Yaou

doi:10.1016/j.cj.2021.07.008

Cited by 19 publications

(18 citation statements)

References 57 publications

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“…Fortunately, this limitation can be overcome with GWAS analysis. Along with high‐density SNP markers and diverse genetic backgrounds, GWAS can provide higher mapping resolution, whereas it may also lead to false positive results due to population structure 59 . Therefore, combining GWAS and QTL mapping has facilitated the study of complex quantitative traits and can improve the validity and credibility of QTLs 60,61 …”

Section: Discussionmentioning

confidence: 99%

Integrated genome‐wide association study and QTL mapping reveals qSa‐3A associated with English grain aphid, Sitobion avenae (Fabricius) resistance in wheat

Zhao

Yan

Zeng

et al. 2023

Pest Management Science

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BACKGROUNDThe English grain aphid, Sitobion avenae (Fabricius), is a devastating pest impacts yield and quality in wheat (Triticum aestivum L.). Breeding resistant wheat varieties and detecting resistance genes are important strategies to control aphid.RESULTSIn this study, we evaluated the number of aphids per spike, the rate of thousand kernel weight decrease and aphid index based on three classic resistance mechanisms (antibiosis, tolerance and antixenosis), and detected SNPs/QTLs for resistance to S. avenae in a natural population of 163 varieties with 20 689 high‐quality single‐nucleotide polymorphism (SNP) markers and recombinant inbred line (RIL) population of 164 lines with 3627 diversity arrays technology (DArT) markers. Results showed that 83 loci significantly associated with S. avenae antibiosis and 182 loci significantly associated with S. avenae tolerance were detected by genome‐wide association study (GWAS), explaining 6.47–15.82% and 8.36–35.61% of the phenotypic variances, respectively. The wsnp_Ku_c4568_8243646 detected in two periods was localized at 34.52 Mb on chromosome 3AS. Then, we confirmed a stable QSa.haust‐3A.2 explained 11.19–20.10% of the phenotypic variances in two periods with S. avenae antixenosis in the physical interval of 37.49–37.50 Mb on chromosome 3A in the RIL population. Therefore, a narrow region in the physical interval of 34.52–37.50 Mb on chromosome 3AS was named as qSa‐3A, which was a new locus between wsnp_Ku_c4568_8243646 and QSa.haust‐3A.2 associated with S. avenae resistance.CONCLUSIONWe found qSa‐3A was a new locus associated with S. avenae resistance. The results could be applied in gene cloning and genetic improvement of S. avenae resistance in wheat. © 2023 Society of Chemical Industry.

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Section: Discussionmentioning

confidence: 99%

Integrated genome‐wide association study and QTL mapping reveals qSa‐3A associated with English grain aphid, Sitobion avenae (Fabricius) resistance in wheat

Zhao

Yan

Zeng

et al. 2023

Pest Management Science

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“…Identi cation of domesticated genes involved in the shaping of the maize ear using joint analysis with GWAS Combined with the candidate genes identi ed by GWAS in two independent inbred maize groups (Xiao et al 2016;Zhang et al 2022), eight candidate domesticated genes related to the ve ear traits were identi ed from the eight QTL (Table 3, Supplemental data 1). While Zm00001d003083 was repeatedly identi ed in qKRN2, qKRN8, qED3, and qCD4, Zm00001d010456 was found to be associated with KRN and KNR in the BP population.…”

Section: Identi Cation Of Domesticated Hotspots Involved In the Shapi...mentioning

confidence: 99%

Profiling the domestication hotspots for ear traits in two maize populations with teosinte gene introgression

Feng

Guan

Yang

et al. 2023

Preprint

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Throughout the history of maize cultivation, ear-related traits have been domesticated. However, little is known about the domesticated genes involved in shaping the ear traits from those of the wild progenitor, teosinte, to those exhibited by modern maize. In this study, five ear traits (kernel row number [KRN], ear length [EL], kernel number per row [KNR], cob diameter [CD], and ear diameter [ED]) were investigated, and eight quantitative trait loci (QTL) hotspots were identified in two maize populations with teosinte gene introgression. We found remarkable enrichment of domesticated and ear-related domesticated genes in qCD1, qCD7, qCD13, qED1, qEL8, qEL10, qKNR11, and qKRN6, suggesting that these eight QTL are domestication hotspots involved in shaping the maize ear from teosinte to modern maize. By combining the QTL identified in this study with the results of the genome-wide association study (GWAS) of ear traits from two association panels, eight candidate domesticated genes related to KRN, KNR, CD, and ED were identified. Considering the expression patterns and sequence variations, Zm00001d025111 and Zm00001d033153, which encode WD40/YVTN and SMAD/FHA proteins, respectively, were proposed as positive regulators of KNR, whereas Zm00001d003083 and Zm00001d005866, which encode isocitrate dehydrogenase and protein disulfide isomerase, respectively, were proposed as negative regulators of KRN. This study presents a frame work for the genomic distribution of ear trait-related and domesticated loci. Several candidate genes with minor effects may be viable targets for further increases in the yield of modern maize.

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“…Compared to sorghum, much more improvements have been made to identify major QTLs or genes for grain yield-related traits in maize. Currently, over 1920 QTLs associated with kernel size and kernel weight reported from 1994 to 2021 have been identified [ 11 , 12 , 44 , 53 , 70 , 71 , 72 , 73 , 83 , 92 , 93 , 94 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 , 122 , 123 , 124 , 125 , 126 , 127 , 128 , 129 , 130 , 131 ]. Among these loci, 528 QTLs related to hundred kernel weight (HKW), 299 QTLs associated with kernel length, 386 QTLs associated with kernel width, 250 QTLs related to kernel thickness, 118 QTLs associated with kernel number per row (KNPR), and 329 QTLs related to kernel row number (KRN) were detected ( Figure 1 c and…”

Section: Genetic Dissection Of Grain Yield-related Traits In Sorghum ...mentioning

confidence: 99%

Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize

Baye

Xie

2022

IJMS

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Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.

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Genetic architecture of maize yield traits dissected by QTL mapping and GWAS in maize

Cited by 19 publications

References 57 publications

Integrated genome‐wide association study and QTL mapping reveals qSa‐3A associated with English grain aphid, Sitobion avenae (Fabricius) resistance in wheat

Integrated genome‐wide association study and QTL mapping reveals qSa‐3A associated with English grain aphid, Sitobion avenae (Fabricius) resistance in wheat

Profiling the domestication hotspots for ear traits in two maize populations with teosinte gene introgression

Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize

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