Identifying favorable alleles for improving key agronomic traits in upland cotton

Abstract Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization.Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1,211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

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Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

10.21203/rs.3.rs-17006/v1 ◽

2020 ◽

Author(s):

De Zhu ◽

Ximei Li ◽

Zhiwei Wang ◽

Chunyuan You ◽

Xinhui Nie ◽

...

Keyword(s):

Upland Cotton ◽

Genetic Improvement ◽

Oil Content ◽

Agronomic Traits ◽

Physical Map ◽

Leaf Shape ◽

Cottonseed Oil ◽

Interval Length ◽

Phenotypic Variance ◽

Multiple Alleles

Abstract Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTLs) in interspecific hybridization. Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1,211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

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Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean

Frontiers in Plant Science ◽

10.3389/fpls.2021.748829 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jessica Delfini ◽

Vânia Moda-Cirino ◽

José dos Santos Neto ◽

Douglas Mariani Zeffa ◽

Alison Fernando Nogueira ◽

...

Keyword(s):

Common Bean ◽

Quantitative Trait ◽

Seed Weight ◽

Genetic Improvement ◽

Agronomic Traits ◽

Genome Wide Association ◽

Multiple Methods ◽

Favorable Alleles ◽

Genome Wide ◽

Multiple Environments

The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.

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Mining favorable alleles for five agronomic traits from the elite rapeseed cultivar zhongshuang 11 by QTL mapping and integration

The Crop Journal ◽

10.1016/j.cj.2020.12.008 ◽

2021 ◽

Author(s):

Xianming Zhou ◽

Lihong Dai ◽

Pengfei Wang ◽

Ying Liu ◽

Zhaoqi Xie ◽

...

Keyword(s):

Qtl Mapping ◽

Agronomic Traits ◽

Favorable Alleles ◽

Rapeseed Cultivar

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Simple sequence repeat markers associated/linked with agronomic traits, as core primers, are eminently suitable for DNA fingerprinting in Upland cotton

Breeding Science ◽

10.1270/jsbbs.17110 ◽

2018 ◽

Vol 68 (4) ◽

pp. 393-403

Author(s):

Chengqi Li ◽

Bihua Chen ◽

Xinjuan Xu ◽

Dandan Li ◽

Jinyuan Dong

Keyword(s):

Dna Fingerprinting ◽

Simple Sequence Repeat ◽

Upland Cotton ◽

Agronomic Traits ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Simple Sequence

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Diallel analysis for agronomic traits in upland cotton in semi-arid zones in Brazil

Genetics and Molecular Research ◽

10.4238/gmr16039677 ◽

2017 ◽

Vol 16 (3) ◽

Cited By ~ 1

Author(s):

D.R. Queiroz ◽

F.J.C. Farias ◽

J.J.C. Vasconcelos ◽

L.P. Carvalho ◽

D.G. Neder ◽

...

Keyword(s):

Upland Cotton ◽

Agronomic Traits ◽

Diallel Analysis ◽

Arid Zones ◽

Semi Arid

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A Diallel Analaysis of Several Agronomic Traits in Upland Cotton ( Gossypium hirsutum L.) 1

Crop Science ◽

10.2135/cropsci1971.0011183x001100010032x ◽

1971 ◽

Vol 11 (1) ◽

pp. 92-96 ◽

Cited By ~ 8

Author(s):

Laval M. Verhalen ◽

Walter C. Morrison ◽

Baha A. Al‐Rawi ◽

Kwee‐Chong Fun ◽

Jay C. Murray

Keyword(s):

Gossypium Hirsutum ◽

Upland Cotton ◽

Agronomic Traits ◽

Gossypium Hirsutum L

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Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China

Journal of Cotton Research ◽

10.1186/s42397-021-00087-3 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Chunping GUO ◽

Zhenyuan PAN ◽

Chunyuan YOU ◽

Xiaofeng ZHOU ◽

Cong HUANG ◽

...

Keyword(s):

Association Mapping ◽

Cotton Fiber ◽

Upland Cotton ◽

Genetic Improvement ◽

Genetic Basis ◽

Agronomic Traits ◽

Complex Trait ◽

Tissue Expression ◽

Cotton Yield ◽

Fiber Yield

Abstract Background Cotton fiber yield is a complex trait, which can be influenced by multiple agronomic traits. Unravelling the genetic basis of cotton fiber yield-related traits contributes to genetic improvement of cotton. Results In this study, 503 upland cotton varieties covering the four breeding stages (BS1–BS4, 1911–2011) in China were used for association mapping and domestication analysis. One hundred and forty SSR markers significantly associated with ten fiber yield-related traits were identified, among which, 29 markers showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4, and 26 markers showed decreased trend effect. Four favorable alleles of 9 major loci (R2 ≥ 3) were strongly selected during the breeding stages, and the candidate genes of the four strongly selected alleles were predicated according to the gene function annotation and tissue expression data. Conclusions The study not only uncovers the genetic basis of 10 cotton yield-related traits but also provides genetic evidence for cotton improvement during the cotton breeding process in China.

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Association Mapping and Domestication Analysis to Dissect Genetic Improvement Process of Upland Cotton Yield-Related Traits in China

10.21203/rs.3.rs-196227/v1 ◽

2021 ◽

Author(s):

GUO Chunping ◽

PAN Zhenyuan ◽

YOU Chunyuan ◽

ZHOU Xiaofeng ◽

HUANG Cong ◽

...

Keyword(s):

Association Mapping ◽

Cotton Fiber ◽

Upland Cotton ◽

Genetic Improvement ◽

Genetic Basis ◽

Agronomic Traits ◽

Complex Trait ◽

Tissue Expression ◽

Cotton Yield ◽

Fiber Yield

Abstract BackgroundCotton fiber yield is a complex trait, which can be influenced by multiple agronomic traits. Unravelling the genetic basis of cotton fiber yield related traits contributes to genetic improvement of cotton fiber. ResultsIn this study, 503 upland cotton varieties covering the 4 breeding stages in China were used to for association mapping and domestication analysis of upland cotton yield-related traits in China. 140 quantitative trait loci (QTLs) significantly associated with ten fiber yield related traits were identified, among which, 29 QTLs showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4, and 26 QTLs showed decreased trend effect. 4 favorable alleles of 9 major QTLs (R2≥3) were strongly selected during the breeding stages, and the candidate genes of the 4 strongly selected alleles were predicated according to the gene function annotation and tissue expression data. ConclusionsThe study not only uncovers the genetic basis of 10 cotton yield related traits, but also provides genetic evidence for cotton improvement during the cotton breeding process in China.

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