Genomic Association and Prediction Study for Yield Traits in a Sugarcane (Saccharum spp. Hybrids) Mapping Population ‘LCP 85‐384’

IF 1.5 4区 农林科学 Q2 AGRONOMY Plant Breeding Pub Date : 2024-09-09 DOI:10.1111/pbr.13221
Theresa Makawa Phiri, Haizheng Xiong, Yong‐Bao Pan, Ryan William Dickson, Neelendra Joshi, Alejandro Rojas, Ainong Shi
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Abstract

Sugarcane (Saccharum spp. hybrids) are complex polyploid and aneuploid interspecific hybrids with 110–130 chromosomes. A traditional sugarcane breeding cycle takes 13–15 years and involves multiple years and locations testing of yield. To identify molecular markers associated with yield‐related traits, the LCP 85‐384 cultivar and its mapping population of 263 self‐progenies were planted in two randomly replicated field plots. The mapping population was genotyped with amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR) and target region amplification polymorphism (TRAP) markers. Data on plant height, stalk number, stalk diameter and stalk weight were collected. A large variation was observed for each trait. A genome‐wide association study (GWAS) was conducted using mixed linear model (MLM), generalized linear model (GLM) and single marker regression (SMR) programmes of TASSEL 5 and FarmCPU of GAPIT 3. A total of 64 yield trait‐associated alleles were identified, including 11 for stalk number, 36 for stalk weight, 21 for stalk diameter and 5 for plant height. Of the 64 alleles, seven were linked to two traits and one to three traits. Genomic prediction (GP) was also performed by cross‐prediction with five models, namely, ridge regression best linear unbiased prediction (rrBLUP), Bayesian ridge regression (BRR), Bayesian A (BA), Bayesian B (BB), and Bayesian least absolute shrinkage and selection operator (BL). Prediction accuracy (r value) reached 0.40 for plant height, 0.36 for stalk number, 0.44 for stalk diameter and 0.54 for stalk weight with the standard errors from 0.009 to 0.012. Once verified, these markers will be a valuable tool to aid in the selection of yield‐related traits in sugarcane improvement programmes.
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甘蔗(蔗属杂交种)制图群体 "LCP 85-384 "产量性状的基因组关联和预测研究
甘蔗(蔗属杂交种)是具有 110-130 条染色体的复杂多倍体和非整倍体种间杂交种。传统的甘蔗育种周期为 13-15 年,涉及多年和多地点的产量测试。为了确定与产量相关性状有关的分子标记,LCP 85-384 栽培品种及其由 263 个自交系组成的测绘群体被种植在两个随机重复的田间小块中。利用扩增片段长度多态性(AFLP)、简单序列重复(SSR)和目标区域扩增多态性(TRAP)标记对制图群体进行了基因分型。收集的数据包括株高、茎秆数、茎秆直径和茎秆重量。在每个性状上都观察到了较大的差异。利用 TASSEL 5 的混合线性模型(MLM)、广义线性模型(GLM)和单标记回归(SMR)程序以及 GAPIT 3 的 FarmCPU,进行了全基因组关联研究(GWAS)。共鉴定出 64 个与产量性状相关的等位基因,包括茎秆数 11 个、茎秆重 36 个、茎秆直径 21 个和株高 5 个。在这 64 个等位基因中,7 个与两个性状相关,1 个与三个性状相关。基因组预测(GP)还通过五个模型进行交叉预测,即脊回归最佳线性无偏预测(rrBLUP)、贝叶斯脊回归(BRR)、贝叶斯 A(BA)、贝叶斯 B(BB)和贝叶斯最小绝对收缩和选择算子(BL)。预测精度(r 值)分别为:株高 0.40、茎秆数 0.36、茎秆直径 0.44 和茎秆重 0.54,标准误差为 0.009 至 0.012。一旦得到验证,这些标记将成为甘蔗改良计划中帮助选择产量相关性状的重要工具。
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来源期刊
Plant Breeding
Plant Breeding 农林科学-农艺学
CiteScore
4.40
自引率
5.00%
发文量
74
审稿时长
3.0 months
期刊介绍: PLANT BREEDING publishes full-length original manuscripts and review articles on all aspects of plant improvement, breeding methodologies, and genetics to include qualitative and quantitative inheritance and genomics of major crop species. PLANT BREEDING provides readers with cutting-edge information on use of molecular techniques and genomics as they relate to improving gain from selection. Since its subject matter embraces all aspects of crop improvement, its content is sought after by both industry and academia. Fields of interest: Genetics of cultivated plants as well as research in practical plant breeding.
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